IP Library › Granted Patent US 12,374,427
Granted Patent B2
US 12,374,427 · App. 17/165,900 · Granted Jul 29, 2025

Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing

Inventors: Pieter Van Rooyen (San Diego, CA); Michael Ruehle (Fort Worth, TX); Rami Mehio (San Diego, CA); Gavin Stone (San Diego, CA); Mark Hahm (San Diego, CA); Eric Ojard (San Francisco, CA); Amnon Ptashek (San Diego, CA)
Assignee: Illumina, Inc.
G16B30/10G16B20/00G16B20/10G16B20/20G16B20/40G16B30/00G16B30/20G16B50/00G16B50/30G16B50/40G16B50/50
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Quick Facts
Patent No.
US 12,374,427
App. No.
17/165,900
Granted
Jul 29, 2025
Kind
B2
Abstract

A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

Claims (69)

1. A nucleic acid sequencing device comprising:

one or more processors;

one or more configurable hardware resources; and

one or more computer readable media each comprising instructions that, when executed by the one or more processors, causes the one or more processors to perform operations that include:

determining, based on a first bar code associated with a first sample, that the first bar code indicates one or more operations that are to be performed on the first sample or first data derived from the first sample;

allocating at least a portion of the one or more configurable hardware resources for use as at least one portion of a genomic analysis pipeline that performs the one or more operations indicated by the first bar code; and

configuring the allocated portion of the one or more configurable hardware resources from a first state that does not include hardware resources configured as the genomic analysis pipeline that performs the determined one or more operations indicated by the first bar code on the first sample or first data derived from the first sample into a second state that includes hardware resources that have been configured as the genomic analysis pipeline that is configured to perform the one or more determined operations indicated by the first bar code on the first sample or the first data derived from the first sample.

2. The nucleic acid sequencing device of claim 1 , wherein determining, based on the first bar code associated with the first sample, that the first bar code indicates one or more operations that are to be performed on the first sample or first data derived from the first sample comprises:

determining one or more operations that are to be performed by accessing a manifest that is indicated by the first barcode.

3. The nucleic acid sequencing device of claim 1 , wherein the first data derived from the first sample is a first genomic read, and wherein the first genomic read derived from the first sample has the same bar code as the first sample.

4. The nucleic acid sequencing device of claim 1 , wherein the hardware resources that have been configured into the second state include a single genomic analysis pipeline.

5. The nucleic acid sequencing device of claim 1 , wherein the hardware resources that have been configured into the second state include multiple genomic analysis pipelines.

6. The nucleic acid sequencing device of claim 1 , wherein the hardware resources that have been configured into the second state include a mapping unit.

7. The nucleic acid sequencing device of claim 1 , wherein the hardware resources that have been configured into the second state include an aligning unit.

8. The nucleic acid sequencing device of claim 1 , wherein the operations further comprise:

providing the first sample or the first data derived from the received first sample as an input to the genomic analysis pipeline of the hardware resources that have been configured into the second state.

9. The nucleic acid sequencing device of claim 1 , wherein the hardware resources that have been configured into the second state include are configured to perform one or more of a primary analysis, secondary analysis, or tertiary analysis.

10. The nucleic acid sequencing device of claim 9 , wherein the primary analysis includes using the nucleic acid sequencing device to perform nucleic acid sequencing of the received first sample to generate a plurality of sequence reads.

11. The nucleic acid sequencing device of claim 9 , wherein the secondary analysis includes one or more of

mapping genomic reads generated based on the first sample,

aligning genomic reads generated based on the first sample to a reference sequence, or

generating a variant call format (VCF) file identifying one or more variants between one or more aligned sequencing reads generated based on the first sample and a reference sequence.

12. The nucleic acid sequencing device of claim 9 , wherein the tertiary analysis includes analysis performed to predict a potential for occurrence of a disease state or analysis performed to determine likelihood of success of a prophylactic or therapeutic modality.

13. The nucleic acid sequencing device of claim 1 , wherein the operations further comprise:

using at least a portion of the hardware resources that have been configured into the second state to perform the one or more operations on at least a portion of the first sample or first data derived from at least a portion of the first sample.

14. A method for configuring a genomic analysis pipeline, the method comprising:

determining, based on a first bar code associated with a first sample, that the first bar code indicates one or more operations that are to be performed on the first sample or first data derived from the first sample;

allocating, based on the determined one or more operations indicated by the first bar code, at least a portion of one or more configurable hardware resources for use as at least one portion of a genomic analysis pipeline that performs the one or more operations indicated by the first bar code; and

configuring the allocated portion of the one or more configurable hardware resources from a first state that does not include hardware resources configured as the genomic analysis pipeline that performs the determined one or more operations indicated by the first bar code on the first sample or first data derived from the first sample into a second state that includes hardware resources that have been configured as the genomic analysis pipeline that is configured to perform the one or more determined operations indicated by the first bar code on the first sample or the first data derived from the first sample.

15. The method of claim 14 , wherein determining, based on the first bar code associated with the first sample, that the first bar code indicates one or more operations that are to be performed on the first sample or first data derived from the first sample comprises:

determining one or more operations that are to be performed by accessing a manifest that is indicated by the first barcode.

16. The method of claim 14 , wherein the first data derived from the first sample is a first genomic read, and wherein the first genomic read derived from the first sample has the same bar code as the first sample.

17. The method of claim 14 , wherein the hardware resources that have been configured into the second state include a single genomic analysis pipeline.

18. The method of claim 14 , wherein the hardware resources that have been configured into the second state include multiple genomic analysis pipelines.

19. The method of claim 14 , wherein the hardware resources that have been configured into the second state include a mapping unit.

20. The method of claim 14 , wherein the hardware resources that have been configured into the second state include an aligning unit.

21. The method of claim 14 , wherein the operations further comprise:

providing the first sample or the first data derived from the received first sample as an input to the genomic analysis pipeline of the hardware resources that have been configured into the second state.

22. The method of claim 14 , wherein the hardware resources that have been configured into the second state include are configured to perform one or more of a primary analysis, secondary analysis, or tertiary analysis.

23. The method of claim 22 , wherein the primary analysis includes using a nucleic acid sequencing device to perform nucleic acid sequencing of the received first sample to generate a plurality of sequence reads.

24. The method of claim 22 , wherein the secondary analysis includes one or more of

mapping genomic reads generated based on the first sample,

aligning genomic reads generated based on the first sample to a reference sequence, or

generating a variant call format (VCF) file identifying one or more variants between one or more aligned sequencing reads generated based on the first sample and a reference sequence.

25. The method of claim 22 , wherein the tertiary analysis includes analysis performed to predict a potential for occurrence of a diseased state or analysis performed to determine likelihood of success of a prophylactic or therapeutic modality.

26. The method of claim 14 , further comprising:

using at least a portion of the hardware resources that have been configured into the second state to perform the one or more operations on at least a portion of the first sample or first data derived from at least a portion of the first sample.

27. One or more non-transitory computer-readable storage media for storing instructions that, when executed by one or more computers, cause the one or more computers to perform operations for configuring a genomic analysis pipeline, the operations comprising:

determining, based on a first bar code associated with a first sample, that the first bar code indicates one or more operations that are to be performed on the first sample or first data derived from the first sample;

allocating, based on the determined one or more operations indicated by the first bar code, at least a portion of one or more configurable hardware resources for use as at least one portion of a genomic analysis pipeline that performs the one or more operations indicated by the first bar code; and

configuring the allocated portion of the one or more configurable hardware resources from a first state that does not include hardware resources configured as the genomic analysis pipeline that performs the determined one or more operations indicated by the first bar code on the first sample or first data derived from the first sample into a second state that includes hardware resources that have been configured as the genomic analysis pipeline that is configured to perform the one or more determined operations indicated by the first bar code on the first sample or the first data derived from the first sample.

28. The computer-readable medium of claim 27 , wherein determining, based on the first bar code associated with the first sample, that the first bar code indicates one or more operations that are to be performed on the first sample or first data derived from the first sample comprises:

determining one or more operations that are to be performed by accessing a manifest that is indicated by the first barcode.

29. The computer-readable medium of claim 27 , wherein the first data derived from the first sample is a first genomic read, and wherein the first genomic read derived from the first sample has the same bar code as the first sample.

30. The computer-readable medium of claim 27 , wherein the hardware resources that have been configured into the second state include a single genomic analysis pipeline.

31. The computer-readable medium of claim 27 , wherein the hardware resources that have been configured into the second state include multiple genomic analysis pipelines.

32. The computer-readable medium of claim 27 , wherein the hardware resources that have been configured into the second state include a mapping unit.

33. The computer-readable medium of claim 27 , wherein the hardware resources that have been configured into the second state include an aligning unit.

34. The computer-readable medium of claim 27 , wherein the operations further comprise:

providing the first sample or the first data derived from the received first sample as an input to the genomic analysis pipeline of the hardware resources that have been configured into the second state.

35. The computer-readable medium of claim 27 , wherein the hardware resources that have been configured into the second state include are configured to perform one or more of a primary analysis, secondary analysis, or tertiary analysis.

36. The computer-readable medium of claim 35 , wherein the primary analysis includes using a nucleic acid sequencing device to perform nucleic acid sequencing of the received first sample to generate a plurality of sequence reads.

37. The computer-readable medium of claim 35 , wherein the secondary analysis includes one or more of

mapping genomic reads generated based on the first sample,

aligning genomic reads generated based on the first sample to a reference sequence, or

generating a variant call format (VCF) file identifying one or more variants between one or more aligned sequencing reads generated based on the first sample and a reference sequence.

38. The computer-readable medium of claim 35 , wherein the tertiary analysis includes analysis performed to predict a potential for occurrence of a diseased state or analysis performed to determine likelihood of success of a prophylactic or therapeutic modality.

39. The computer-readable medium of claim 27 , wherein the operations further comprising:

using at least a portion of the hardware resources that have been configured into the second state to perform the one or more operations on at least a portion of the first sample or first data derived from at least a portion of the first sample.

Assignments (4)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 18, 2025
From: EDICO GENOME CORPORATION
To: ILLUMINA SOFTWARE, INC.
Reel/Frame 071452/0860 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 18, 2025
From: ILLUMINA SOFTWARE, INC.
To: ILLUMINA, INC.
Reel/Frame 071452/0898 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Apr 4, 2025
From: VAN ROOYEN, PIETRE; RUEHLE, MICHAEL; MEHIO, RAMI; STONE, GAVIN; HAHM, MARK DAVID; OJARD, ERIC; PTASHEK, AMNON
To: EDICO GENOME CORPORATION
Reel/Frame 070736/0611 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Apr 12, 2021
From: VAN ROOYEN, PIETER; RUEHLE, MICHAEL; MEHIO, RAMI; STONE, GAVIN; HAHM, MARK DAVID; OJARD, ERIC; PTASHEK, AMNON
To: EDICO GENOME CORPORATION
Reel/Frame 055896/0557 →
Continuity (12)
Continuation 15915013 · Mar 7, 2018
Continuation 15643381 · Jul 6, 2017
Continuation 15616833 · Jun 7, 2017
Continuation In Part 15497149 · Apr 25, 2017
Continuation In Part 15404146 · Jan 11, 2017
Provisional Application 62469442 · Mar 9, 2017
Provisional Application 62462869 · Feb 23, 2017
Provisional Application 62414637 · Oct 28, 2016
Provisional Application 62399582 · Sep 26, 2016
Provisional Application 62347080 · Jun 7, 2016
Provisional Application 62277445 · Jan 11, 2016
Related Publication 20210257052A1 · Aug 19, 2021
References Cited (356)
US 5859972A · Subramaniam · 1999 [cited by applicant]
US 5964072A · Rasmussen et al. · 1999 [cited by applicant]
US 5964860A · Peterson et al. · 1999 [cited by applicant]
US 6112288A · Ullner · 2000 [cited by applicant]
US 6253529B1 · De Boer et al. · 2001 [cited by applicant]
US 6681186B1 · Denisov · 2004 [cited by applicant]
US 7135701B2 · Amin et al. · 2006 [cited by applicant]
US 7533068B2 · Maassen et al. · 2009 [cited by applicant]
US 7680790B2 · Indeck et al. · 2010 [cited by applicant]
US 7917299B2 · Buhler et al. · 2011 [cited by applicant]
US 7917302B2 · Rognes · 2011 [cited by applicant]
US 7945668B1 · Nucci et al. · 2011 [cited by applicant]
US 7948015B2 · Rothberg · 2011 [cited by applicant]
US 7969805B2 · Thom et al. · 2011 [cited by applicant]
US 8190548B2 · Choi · 2012 [cited by applicant]
US 8195596B2 · Rose et al. · 2012 [cited by applicant]
US 8209130B1 · Kennedy et al. · 2012 [cited by applicant]
US 8217433B1 · Fife et al. · 2012 [cited by applicant]
US 8280640B2 · Levin et al. · 2012 [cited by applicant]
US 8445945B2 · Rothberg et al. · 2013 [cited by applicant]
US 8524487B2 · Fife et al. · 2013 [cited by applicant]
US 8558288B2 · Rothberg et al. · 2013 [cited by applicant]
US 8560282B2 · Macready et al. · 2013 [cited by applicant]
US 8594951B2 · Homer · 2013 [cited by applicant]
US 8620923B1 · Wormley et al. · 2013 [cited by applicant]
US 8700689B2 · Macready et al. · 2014 [cited by applicant]
US 8738105B2 · Berkley et al. · 2014 [cited by applicant]
US 8751166B2 · Friedlander et al. · 2014 [cited by applicant]
US 8936763B2 · Rothberg et al. · 2015 [cited by applicant]
US 9014989B2 · McMillen et al. · 2015 [cited by applicant]
US 9026574B2 · Macready et al. · 2015 [cited by applicant]
US 9235680B2 · Van Rooyen et al. · 2016 [cited by applicant]
US 9322872B2 · Hill · 2016 [cited by applicant]
US 9355365B2 · Berkley et al. · 2016 [cited by applicant]
US 9405876B2 · Macready et al. · 2016 [cited by applicant]
US 9483610B2 · Mcmillen et al. · 2016 [cited by applicant]
US 9576103B2 · Mcmillen et al. · 2017 [cited by applicant]
US 9618474B2 · Van Rooyen et al. · 2017 [cited by applicant]
US 9679104B2 · Van Rooyen et al. · 2017 [cited by applicant]
US 9792405B2 · Van Rooyen et al. · 2017 [cited by applicant]
US 10068183B1 · Van Rooyen et al. · 2018 [cited by applicant]
US 20020086161A1 · Kamatani et al. · 2002 [cited by applicant]
US 20030033279A1 · Gibson et al. · 2003 [cited by applicant]
US 20030033501A1 · Cooke · 2003 [cited by applicant]
US 20030039362A1 · Califano et al. · 2003 [cited by applicant]
US 20030104470A1 · Fors et al. · 2003 [cited by applicant]
US 20040024536A1 · Rognes et al. · 2004 [cited by applicant]
US 20040059721A1 · Patzer · 2004 [cited by applicant]
US 20040098203A1 · Rognes et al. · 2004 [cited by applicant]
US 20040126840A1 · Cheng et al. · 2004 [cited by applicant]
US 20040142463A1 · Walker et al. · 2004 [cited by applicant]
US 20050060195A1 · Bessette · 2005 [cited by applicant]
US 20050131649A1 · Larsen et al. · 2005 [cited by applicant]
US 20050228595A1 · Cooke et al. · 2005 [cited by applicant]
US 20060225165A1 · Maassen et al. · 2006 [cited by applicant]
US 20070038381A1 · Melchior et al. · 2007 [cited by applicant]
US 20070078897A1 · Hayashi et al. · 2007 [cited by applicant]
US 20070088510A1 · Li et al. · 2007 [cited by applicant]
US 20070196816A1 · Schwartz · 2007 [cited by applicant]
US 20080005024A1 · Kirkwood et al. · 2008 [cited by applicant]
US 20080050782A1 · Selifonov et al. · 2008 [cited by applicant]
US 20080086274A1 · Chamberlain et al. · 2008 [cited by applicant]
US 20080176750A1 · Rose et al. · 2008 [cited by applicant]
US 20080250016A1 · Farrar et al. · 2008 [cited by applicant]
US 20090121215A1 · Choi et al. · 2009 [cited by applicant]
US 20090125248A1 · Shams et al. · 2009 [cited by applicant]
US 20090171647A1 · Mannava et al. · 2009 [cited by applicant]
US 20090253130A1 · Yoo · 2009 [cited by applicant]
US 20090270277A1 · Glick et al. · 2009 [cited by applicant]
US 20100077267A1 · Perego et al. · 2010 [cited by applicant]
US 20100082805A1 · Orton et al. · 2010 [cited by applicant]
US 20100085827A1 · Thom · 2010 [cited by applicant]
US 20100169313A1 · Kenedy et al. · 2010 [cited by applicant]
US 20100281401A1 · Tebbs et al. · 2010 [cited by applicant]
US 20100327847A1 · Leiber et al. · 2010 [cited by applicant]
US 20110004413A1 · Carnevali · 2011 [cited by applicant]
US 20110093581A1 · Ventatachalm · 2011 [cited by applicant]
US 20110184235A1 · Schostek et al. · 2011 [cited by applicant]
US 20110227043A1 · Guo · 2011 [cited by applicant]
US 20120001615A1 · Levine · 2012 [cited by applicant]
US 20120089339A1 · Ganeshalingam et al. · 2012 [cited by applicant]
US 20120102041A1 · Park et al. · 2012 [cited by applicant]
US 20120109849A1 · Chamberlain · 2012 [cited by applicant]
US 20120135394A1 · Kim · 2012 [cited by examiner]
US 20120149981A1 · Khait et al. · 2012 [cited by applicant]
US 20120214172A1 · Chen et al. · 2012 [cited by applicant]
US 20130018599A1 · Peng et al. · 2013 [cited by applicant]
US 20130091121A1 · Galinsky · 2013 [cited by applicant]
US 20130110407A1 · Baccash et al. · 2013 [cited by applicant]
US 20130124100A1 · Drmanac · 2013 [cited by applicant]
US 20130144925A1 · Macready · 2013 [cited by applicant]
US 20130157870A1 · Pushkarev et al. · 2013 [cited by applicant]
US 20130194882A1 · Ishii et al. · 2013 [cited by applicant]
US 20130204851A1 · Bhola et al. · 2013 [cited by applicant]
US 20130245958A1 · Forster et al. · 2013 [cited by applicant]
US 20130254202A1 · Friedlander et al. · 2013 [cited by applicant]
US 20130275486A1 · Dickinson et al. · 2013 [cited by applicant]
US 20130296175A1 · Rafnar et al. · 2013 [cited by applicant]
US 20130297221A1 · Johnson et al. · 2013 [cited by applicant]
US 20130307029A1 · Xu et al. · 2013 [cited by applicant]
US 20130311106A1 · White et al. · 2013 [cited by applicant]
US 20130316331A1 · Isakov · 2013 [cited by applicant]
US 20130324417A1 · Kennedy et al. · 2013 [cited by applicant]
US 20130332081A1 · Reese et al. · 2013 [cited by applicant]
US 20130338012A1 · Sulem et al. · 2013 [cited by applicant]
US 20130338934A1 · Asadi · 2013 [cited by examiner]
US 20140024537A1 · Rigatti et al. · 2014 [cited by applicant]
US 20140033125A1 · Merel et al. · 2014 [cited by applicant]
US 20140045705A1 · Bustamante et al. · 2014 [cited by applicant]
US 20140046926A1 · Walton · 2014 [cited by applicant]
US 20140051588A9 · Drmanac et al. · 2014 [cited by applicant]
US 20140081665A1 · Holmes · 2014 [cited by applicant]
US 20140114582A1 · Mittelman et al. · 2014 [cited by applicant]
US 20140121116A1 · Richards · 2014 [cited by applicant]
US 20140164516A1 · Maltbie · 2014 [cited by applicant]
US 20140200166A1 · Van Rooyen et al. · 2014 [cited by applicant]
US 20140236490A1 · Van Rooyen et al. · 2014 [cited by applicant]
US 20140297196A1 · Olson · 2014 [cited by applicant]
US 20140304276A1 · Boyce · 2014 [cited by applicant]
US 20140309944A1 · Van Rooyen et al. · 2014 [cited by applicant]
US 20140310215A1 · Trakadis · 2014 [cited by applicant]
US 20140316716A1 · Jiang et al. · 2014 [cited by applicant]
US 20140337052A1 · Pellini et al. · 2014 [cited by applicant]
US 20140350968A1 · Hahn et al. · 2014 [cited by applicant]
US 20140368550A1 · Vaske et al. · 2014 [cited by applicant]
US 20140371109A1 · McMillen et al. · 2014 [cited by applicant]
US 20140371110A1 · Van Rooyen et al. · 2014 [cited by applicant]
US 20150066824A1 · Harris et al. · 2015 [cited by applicant]
US 20150123600A1 · Graot et al. · 2015 [cited by applicant]
US 20150142334A1 · Mishra et al. · 2015 [cited by applicant]
US 20150144109A1 · Mukaihara et al. · 2015 [cited by applicant]
US 20150154406A1 · Naehrig et al. · 2015 [cited by applicant]
US 20150211055A1 · Apte et al. · 2015 [cited by applicant]
US 20150248525A1 · Ury et al. · 2015 [cited by applicant]
US 20150286495A1 · Lee et al. · 2015 [cited by applicant]
US 20150310163A1 · Kingsmore et al. · 2015 [cited by applicant]
US 20150166389A1 · Dimitrova et al. · 2015 [cited by applicant]
US 20150339437A1 · McMillen et al. · 2015 [cited by applicant]
US 20150363550A1 · Green et al. · 2015 [cited by applicant]
US 20160046986A1 · Eltoukhy et al. · 2016 [cited by applicant]
US 20160057246A1 · Krishnaiahsetty · 2016 [cited by applicant]
US 20160092631A1 · Yandell et al. · 2016 [cited by applicant]
US 20160140290A1 · Van Rooyen et al. · 2016 [cited by applicant]
US 20160171153A1 · Van Rooyen et al. · 2016 [cited by applicant]
US 20160178569A1 · Hoffman et al. · 2016 [cited by applicant]
US 20160283407A1 · Van Rooyen et al. · 2016 [cited by applicant]
US 20160306923A1 · Van Rooyen et al. · 2016 [cited by applicant]
US 20170270245A1 · Van Rooyen et al. · 2017 [cited by applicant]
US 20170308644A1 · Van Rooyen et al. · 2017 [cited by applicant]
US 20180121601A1 · Hahm et al. · 2018 [cited by applicant]
US 20180196916A1 · Van Rooyen et al. · 2018 [cited by applicant]
US 20180196917A1 · Van Rooyen et al. · 2018 [cited by applicant]
US 20180239865A1 · Van Rooyen et al. · 2018 [cited by applicant]
US 20180240032A1 · Van Rooyen · 2018 [cited by applicant]
US 20180189444A1 · Van Rooyen et al. · 2018 [cited by applicant]
US 20190171963A1 · Van Rooyen et al. · 2019 [cited by applicant]
US 20190172558A1 · Van Rooyen et al. · 2019 [cited by applicant]
AU 2014335877 · 2016 [cited by applicant]
CN 102308206A · 2012 [cited by applicant]
CN 102521528A · 2012 [cited by applicant]
CN 103293209A1 · 2013 [cited by applicant]
CN 104428425A · 2015 [cited by applicant]
CN 105051741B · 2018 [cited by applicant]
EP 2313523A2 · 2011 [cited by applicant]
JP 2007108949A · 2007 [cited by applicant]
JP 2007512808A · 2007 [cited by applicant]
JP 2016514291 · 2016 [cited by applicant]
JP 2014146318A · 2021 [cited by applicant]
KR 1020130088512A · 2013 [cited by applicant]
RU 2282242 · 2006 [cited by applicant]
RU 2015144109 · 2017 [cited by applicant]
WO WO2011149534A2 · 2011 [cited by applicant]
WO WO2012122546A2 · 2012 [cited by applicant]
WO WO2013128371A2 · 2013 [cited by applicant]
WO WO2014060305A1 · 2014 [cited by applicant]
WO WO2014074246A1 · 2014 [cited by applicant]
WO WO2014113736A1 · 2014 [cited by applicant]
WO WO2014121091A1 · 2014 [cited by applicant]
WO WO2014186604A1 · 2014 [cited by applicant]
WO WO2015051006A2 · 2015 [cited by applicant]
WO WO2015089333A1 · 2015 [cited by applicant]
WO WO2015100427A1 · 2015 [cited by applicant]
WO WO2015123600A1 · 2015 [cited by applicant]
WO WO2015166389A1 · 2015 [cited by applicant]
WO WO2016051429 · 2016 [cited by applicant]
WO WO2016061396A1 · 2016 [cited by applicant]
WO WO2002086161 · 2022 [cited by applicant]
WO WO2015166389 · 2022 [cited by applicant]
Abbas, N., et al., “Combining Executin Pipelines to Improve Parallel Implementation of HMMER on FPGA,” Microprocessors and Microsystems 39(7), Jun. 25, 2015, 457-470. [cited by applicant]
Altera Corp, Implementation of the Smith-Waterman Algorithm on a Reconfigurable Supercomputing Platform, White Paper, 18 pgs Sep. 2007 Ver. 1. [cited by applicant]
Alachiotis, et al, Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs, The Exelixis Lab, (2011) pp. 8, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. [cited by applicant]
Angiuoli et al., “Mugsy: fast multiple alignment of closely related whole genomes,” Bio informatics (2011) 27 (3): 334-342. First published on line: Dec. 9, 2010. http://bioinformatics.oxfordjoumals.org/content/27/31334… [cited by applicant]
Anonymous: “FPGA-accelerated Bioinformics at #ASHG-Dragen Aligner from Edico Genome.” Oct. 20, 2014 (Oct. 20, 2014). XP055360856. Retrieved from the internet: URL:http://moolog.us/blogs/glob/2014/210/20/fpga-accelerated… [cited by applicant]
AU Office Action in Australian Appln. No. 2017207317, dated Sep. 3, 2021, 6 pages. [cited by applicant]
Benkrid et al, A highly parameterized and efficient FPGA-based skeleton for pairwise biological sequence alignment, IEEE Transactions on VLSI Systems, Apr. 2009, pp. 561-570 (1-12), IEEE Educational Activities Dept. Pis… [cited by applicant]
Benkrid et al. Review Article: “High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP.” Hindawi Publishing Corporation. International Journal of Reconfigurable Computing. vol… [cited by applicant]
Benkrid, Khaled, et. al. “A High Performance Reconfigurable Core for Motif Searching Using Profile HMM.” NASA ESA Conference on Adaptive Hardware and Systems, IEEE, 2008. pp. 285-292. [cited by applicant]
Buyukkurt et al, Compiler Generated Systolic Arrays for Wavefront Algorithm Acceleration on FPGAs, Sep. 2008, 4 pgs, International Conference on Field Programmable Logic and Applications, Heidelberg, Germany. [cited by applicant]
Carneiro, Mauricio. “Accelerating Variant Calling.” Broad Institute, Intel Genomic Sequencing Pipeline Workshop, Powerpoint Presentation, Mount Sinai, Dec. 10, 2013. 26 pages. [cited by applicant]
Chang Mau-Chung Frank et al: “The SMEM Seeding Acceleration for DNA Sequence Alignment.” 2016 IEEE 24th Annual International Symposium on Fieldprogrammable Custom Computing Machines (FCCM), IEEE, [retrieved on Aug. 16, … [cited by applicant]
Chang, et al., Exploring Sequence Alignment Algorithms on FPGA-based Heterogeneous B Architectures, Proceedings IWBBIO, pp. 330-341, 2014, Granada. [cited by applicant]
Chang, Xin, et al. “FPGA-based Heterogeneous Architecture for Sequence Alignment.” (2014) 4 pages. [cited by applicant]
Choi, J., et al.“Impact of Cache Architectures and Interface on Performance and Area of FPGA-Based Processor/Parallel-Accelerator Systems,” FCCM, IEEE, Apr. 29, 2012, 17-24. [cited by applicant]
Chrysanthou et. al. “Parallel Accelerators for GlimmerHMM Bioinformatics Algorithm.” 2011 Design, Automation & Test in Europe Conference & Exhibition, IEEE, 2011. 6 pages. [cited by applicant]
Chrysos et al., “Reconfiguring the bioinformatics computational spectrum: Challenges and opportunities of fpga-based bioinformatics acceleration platforms,” IEEE Design & Test, Oct. 2, 2013, 31(1):62-73. [cited by applicant]
CN Office Action in Chinese Appln. No. 201780006359.1, dated Jul. 30, 2021, 37 pages (with English translation). [cited by applicant]
Derrien et al. Fast Computation and Applications of Genome Mappability. PLOS One. Published: Jan. 19, 2012. 15 pages. http://joumals.plos.org/plosone/article?id=10.1371/journal.pone.0030377. Retrieved May 25, 2016. [cited by applicant]
Deutsch, D. “Quantum theory, the Church-Turing principle and the universal quantum computer.” Proceedings of the Royal Society of London A 400, pp. 97-117 (1985). Printed in Great Britain. [cited by applicant]
Dilthey et al., “Improved genome inference in the MHC using a population reference graph,” Nature Genetics 47, 2015. 682-8. [cited by applicant]
Dydel, Stefan and Piotr Bala. “Large Scale Protein Sequence Alignment Using FPGA Reprogrammable Logic Devices.” Faculty of Mathematics and Computer Science. N. Copernicus University, 1 O pgs, 2004, Torun, Poland.J. Beck… [cited by applicant]
EP Extended Search Report in European Appln. No. 21179125.5, dated Nov. 29, 2021, 9 pages. [cited by applicant]
EP Office Action in European U.S. Appl. No. 17/731,690, dated Jan. 4, 2020, 19 pages. [cited by applicant]
Eusse, et al.“A Protein Sequence Analysis Hardwar Accelerator Based on Divergences,” International Journal of Reconfigurable Computing, Jan. 1, 2012, 19 pages. [cited by applicant]
Faes, et al, Scalable Hardware Accelerator for Comparing DNA and Protein Sequences, INFOSCALE, 2006, pp. 6, ACM, Hong Kong. [cited by applicant]
Fagin, FPGA and Rapid Prototyping Technology Use in a Special Purpose Computer for Molecular Genetics, Website: http://www.faginfamily.net/barry/Papers/ICCD92.htm, Thayer School of Engineering, Dartmouth, Hanover, NH. (… [cited by applicant]
Fernandez et al. “Multithreaded FPGA Acceleration of DNA Sequence Mapping.” University of California Riverside, Riverside and Jacquard Computing Inc. Riverside. 2012 IEEE. 6 pages. [cited by applicant]
Fernandez et al. PowerPoint presentation on “Multithreaded FPGA Acceleration of DNA Sequence Mapping.” UC Riverside, Department of Computer Science and Engineering Jacquard Computing. 2012. 20 pages. [cited by applicant]
Fernandez, W. Najjar, E. Harris, and S. Lonardi. Exploration of Short Reads Genome Mapping in Hardwares. Field Programmable Logic and Applications (FPL), 20th Int. Conf. Milano, Italy, Aug. 2010. 4 pages. [cited by applicant]
Ferraz, Samuel and Nahri Moreano. “Evaluating Optimization Strategies for HMMer Acceleration on GPU.” 2013 International Conference on Parallel and Distributed Systems, IEEE, 2013. pp. 59-68. [cited by applicant]
Feynman, Richard P. “Simulating Physics with Computers.” International Journal of Theoretical Physics, vol. 21, Nos. 617, (1982): pp. 467-488. [cited by applicant]
Fromer et al., “Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth,” The American Journal of Human Genetics, Oct. 5, 2012, 91(4):597-607. [cited by applicant]
Giraldo, J., et al., “A HMMER Hardware Accelerator using Divergences,” 2010 Design, Automation & Test in Europe Conference and Exhibition, Mar. 12, 2010 405-10. [cited by applicant]
Guccione et al, Gene Matching Usina JBits, Xilinx, Inc. San Jose CA (2002), 9 pages. [cited by applicant]
Hall, Adam. “Short-Read DNA Sequence Alignment with Custom Designed FPGA-based Hardware.” Master of Science Thesis. The University of Cambridge, 2007. 186 pages. [cited by applicant]
Hardcastle and K. Kelly. baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data. Published Aug. 10, 2010, BMC Bioinformatics http://bmcbioinformatics.biomedcentral.com/ article… [cited by applicant]
Harris, B. et al., “A Banded Amith-Waterman FPGA Accelerator For Mercury BLASTP”, SECS Technology, Inc, 2007, 5 pages. [cited by applicant]
Hasan et al, An Overview of Hardware-Based Acceleration of Biological Sequence Alignment, Computational Biology and Applied Bioinformatics, Sep. 2011, Tech, Rijeka, Croatia, 187-202. [cited by applicant]
Herbordt, Martin et al., “Single Pass Streaming BLAS on FPGAs”, NIH Public Access Author Manuscript, Nov. 2007, Parallel Comput, 25 pages. [cited by applicant]
Herbordt, Martin, et al., “Single Pass, BLAST-like, Approximate String Matching of FPGAs”, Boston University, 2006, 19 pgs, Boston. [cited by applicant]
Hoang et al., FPGA Implementation of Systolic Sequence Alignment, 1991, 4 pgs NSF Graduate Fellowship. [cited by applicant]
Hoang, A Systolic Array for the Sequence Alignment Problem, Apr. 1992, 25 pgs, Brown University, Providence, RI. [cited by applicant]
Hoang, Searching Genetic Databases on Splash 2, FCCM20 Endorsement, 1993, pp. 185-191, Brown University, Providence, RI. [cited by applicant]
Holt et al., “MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects,” BMC Bioinformatics, Dec. 2011, 12(1):1-4. [cited by applicant]
Homer, B. Merriman, and S. Nelson. BFAST: An Alignment Tool for Large Scale Genome Resequencing. PLOS. Mar. 14, 2011. http://journals.plos.org/plosone/article?id=10.1371/joumal.pone.0007767. Retrieved May 25, 2016. 11 p… [cited by applicant]
Huang, Sitao, et. al. “Hardware Acceleration of the Pair-HMM Algorithm for DNA Variant Calling.” Proceedings of the 2017 ACMISIGDA International Symposium on Field-Programmable Gate Arrays, Feb. 22-24, 2017, Monterey, C… [cited by applicant]
Hughey, Parallel Hardware For Sequence Comparison And Alignment, Cabios, 1996, pp. 473-479, vol. 12 No. 6, Oxford University Press, CA. [cited by applicant]
PCT International Search Report and Written Opinion issued in International Application No. PCT/US2017/013057, mailed Apr. 11, 2017 (Nov. 4, 2017). 10 pages. [cited by applicant]
International Search Report and Written Opinion issued in International Application No. PCT/US2017/036424, mailed Sep. 12, 2017 (Dec. 9, 2017). 12 pages. [cited by applicant]
International Search Report and Written Opinion issued in International Application No. PCT/US2017/040385, mailed Oct. 27, 2017 (Oct. 27, 2017). 15 pages. [cited by applicant]
International Search Report and Written Opinion issued in International Application No. PCT/US2017/058890, mailed Feb. 23, 2018 (Feb. 23, 2018). 16 pages. [cited by applicant]
International Search Report dated Jun. 18, 2014, for PCT application No. PCT/US2014/012144. 2 pages. [cited by applicant]
Isa, Nazrin M., et al. “A Novel Efficient FPGA Architecture for HMM ER Acceleration.” 2012 International Conference on Reconfigurable Computing and FPGAs (ReConFig), IEEE, 2013. 6 pages. [cited by applicant]
Isaac TS Li et al. Methodology article, 160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA). Published Jun. 7, 2007. BMC Bioinformatics 2007, 8:185, Institute of Biomateria… [cited by applicant]
Jacob, Arpith et al. “FPGA-Accelerated seed generation in Mercury BLASTP”, Washington University in St. Louis, BECS Technology Inc. (2007). 10 oas. [cited by applicant]
Jacob, Arpith, et al. “Preliminary Results in Accelerating Profile HMM Search on FPGAs.” In Proceedings of 6th IEEE International Workshop on High Performance Computational Biology, Mar. 2007. 9 pages. [cited by applicant]
JP Japanese Office Action in Japanese Appln. No. 2018-564374, dated Oct. 4, 2021, 7 pages (with English translation). [cited by applicant]
Junid et al. “Development of Novel Data Compression Technique for Accelerate DNA Sequence Alignment Based on Smith-Waterman Algorithm.” Highlighted. University Technology MARA (UiTM). 2009 Third UKSim European Symposium… [cited by applicant]
Junid et al. “Optimization of DNA Sequences Data for Accelerate DNA Sequences Alignment on FPGA.” University Technology MARA (UiTM). 2010 Fourth Asia International Conference on Mathematical/Analytical Modelling and Com… [cited by applicant]
Kasap, Server et al, “Design and Implementation of an FPGA-based Core for Gapped BLAST Sequence Alignment with the Two-Hit Method”, Engineering Letters, 16:3 EL 16 3 25, Aug. 20, 2012, 10 pgs, Scotland, UK (2008). [cited by applicant]
Lancaster Joseph, “Design and Evaluation of a BLAST Ungapped Extension Accelerator, Master's Thesis”, Washington University, Jan. 1, 2006, 79 pgs, Report No. WUCSE-20016-21, 2006 St. Louis. [cited by applicant]
Lancaster Joseph, et al. “Acceleration of Ungapped Extension in Mercury BLAST”, MSP-7th Workshop on Media and Streaming Processors, Nov. 2005, 9 pgs. [cited by applicant]
Langmead et al. Searching for SNPs with cloud computing. Genome Biology 2009, vol. 10:1ss, II: R134, Published: Nov. 20, 2009. 10 pages. [cited by applicant]
Lavenier, Dominque. “SAMBA: Systolic Accelerator for Molecular Biological Applications.” Research Report RR-2845, Inria. 22 pgs, Mar. 1996, France. [cited by applicant]
Lee et al., “Clinical exome sequencing for genetic identification of rare Mendelian disorders,” Jama, Nov. 12, 2014, 312(18):1880-7. [cited by applicant]
Lemoine, et al, High Speed Pattern Matching in Genetic Data Base with Reconfigurable Hardware, ISMB-94 Proceedings, 1994, pas 269-275, AAAI (www.aaai.org), France. [cited by applicant]
Liu et al. “An FPGA-Based Web Server for High Performance Biological Sequence Alignment.” The University of Edinburgh, Edinburgh, UK and The Queen's University of Belfast, Northern Ireland, UK. 2009 NASA/ESA Conference … [cited by applicant]
Lloyd, S. et al., “Hardware Accelerated Sequence Alignment with Traceback”, Department of Computer Science, BYU, vol. 2009 (762362), 2009, 10 pages. [cited by applicant]
Lopresti, Rapid Implementation of a Genetic Sequence Comparator Using Field-Programmable Logic Arrays, Advanced Research in VLSI, 1991, pp. 138-152, UC Santa Cruz, CA. [cited by applicant]
Madhavan, Advait, et. al. “Race Logic: A Hardware Acceleration for Dynamic Programming Algorithms.” 2014 ACM/IEEE 41st Intrenational/ Symposium on Computer Architecture (ISCA), IEEE, 2014. 12 pages. [cited by applicant]
Mahram, FPGA Acceleration of Sequence Analysis Tools in Bioinformatics, Dissertation, 2013, 180 paaes, Boston, MA. [cited by applicant]
Maxfield. Impulse achieves 16X speed-up of genome analysis on $2,500 FPGA module. EE Times. Jun. 15, 2012. http://www.eetimes.com/ documentasp?doc id=1317288&print=yes. Retrieved Mar. 29, 2016. 4 pages. [cited by applicant]
McKenna et al., “The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data,” Genome Research, Sep. 1, 2010, 20(9):1297-303. [cited by applicant]
Mikami, et al, Efficient FPGA-based Hardware Algorithms for Approximate String Matching, ITC-CSCC, 2008, pp. 201-204, Hiroshima, JP. [cited by applicant]
Miller, Neil A. et al. “A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases.” Genome Medicine. vol. 7, No. 100, Sep. 30, 2015 (Sep. 30, 2015). 16 pages. [cited by applicant]
Mishra, “Gappy TotalReCaller for RNASeq Base-Calling and Mapping,” bioRxiv, Jan. 1, 2013, 000489, 10 pages. [cited by applicant]
Moritz, et al, Implementation of a Parallel Algorithm for Protein Pairwise Alignment Using Reconfigurable Computing, Conference date 2006, Published Feb. 12, 2007. pp. 7, Brazilian National Research Council (CNPq), Braz… [cited by applicant]
Muriki, Krishna et al., “RC-BLAST: Towards a Portable, Cost-Effective Open Source Hardware Implementation” Supported in part by NSF Grant EIA-9985986, (2005). 8 pgs. [cited by applicant]
Nawaz, et al., A Parallel FPGA Design of the Smith-Waterman Traceback, Conference date 2010. Published Jan. 6, 2011, pp. 6, ACE Associated Compiler Expert, The Netherlands. [cited by applicant]
Nawaz, et al, Fast Smith-Waterman hardware implementation, hArtes (IST-035143), (2010) pp. 4, The Morpheus (IST-027342) and RCOSY (DES-6392) Projects. [cited by applicant]
Nelson, et al., Shepard: A Fast Exact Match Short Read Aligner, Research Report, (2012) pp. 4, Dept. of Electrical and Computer Engineering, Iowa State University, Ames, IA. [cited by applicant]
Oliver et al. “Multiple Sequence Alignment on an FPGA.” IEEE Computer Society. School of Computer Engineering, Nanyang Technological University, Singapore; Project Proteus, School of Engineering, Ngee Ann Polytechnic, S… [cited by applicant]
Oliver et al., “A Reconfigurable Computing System Based on a Cache-Coherent Fabric,” Rconfig, IEEE, Nov. 30, 2011, 6 pages. [cited by applicant]
Oliver et al., “Integrating FPGA acceleration into HMMer,” Parallel Computing, Elsevier, Sep. 20, 2008, 681-91. [cited by applicant]
Oliver, et al, Using Reconfigurable Hardware to Accelerate Multiple Sequence Alignment with ClustalW, Bioinformatics, 2005, pp. 3431-3432, vol. 21 No. 16, Advanced Access Publication, Singapore. [cited by applicant]
Oliver, Hyper Customized Processors for Bio-Sequence Database Scanning on FPGAs, FPGA, pp. 229-237, 2005 Monterey, CA. [cited by applicant]
Olson et al. “Hardware Acceleration of Short Read Mapping.” University of Washington, Pico Computing Inc., Fred Hutchinson Cancer Research Center Seattle, WA. 2012. 8 pages. [cited by applicant]
Olson, Corey Bruce. “An FPGA Acceleration of Short Read Human Genome Mapping.” Master II of Science Thesis. University of Washington, 2011. 103 pages. [cited by applicant]
PCT International Search Report and Written Opinion in International Appln. No. PCT/US2016/020480, dated May 17, 2016. [cited by applicant]
PCT International Search Report and Written Opinion in International Appln. No. PCT/US2016/026796, dated Jul. 18, 2016. [cited by applicant]
PCT International Search Report and Written Opinion in International Appln. No. PCT/US2016/040842, dated Oct. 4, 2016. [cited by applicant]
PCT International Search Report and Written Opinion in International Appln. No. PCT/US2016/18765, dated May 6, 2016. [cited by applicant]
Peltenburg, Johan, et al. “Maximizing Systolic Array Efficiency to Accelerate the PairHMM Forward Algorithm.” 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBMJ, IEEE) 2016. pp. 758-762. [cited by applicant]
Raphael, 8. , et al., “A novel method for multiple alignment of sequences with repeated and shuffled elements”, Genome Research 14(11 ), Nov. 1, 2004, 2336-2346. [cited by applicant]
Ren, Shanshan, et al. “FPGA Acceleration of the Pair-HM Ms Forward Algorithm for DNA Sequence Analysis.” 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, 2015. 6 pages. [cited by applicant]
Rimmer et al., “Integrating mapping-, assembly-and haplotype-based approaches for calling variants in clinical sequencing applications,” Nature Genetics, Aug. 2014, 46(8):912-8. [cited by applicant]
Ruffalo, T. LaFramboise, and M. Koyuturk. Comparative analysis of algorithms for nextgeneration sequencing read alignment. Bioinformatics (2011) 27 (20): 2790-2796. First published online: Aug. 19, 2011. https://bioinfo… [cited by applicant]
Russell, “TGAC Unleashes DRAGEN to Accelerate Genomics Workflows”, HPC Wire, dated Oct. 28, 2015, retrieved Apr. 12, 2022 form URL <https://www.hpcwire.com/2015/10/28/tgac-unleashes-dragen-to-accelerate-genomics-workflo… [cited by applicant]
Sakar, Souradip et al. “Network-on-Chip Hardware Accelerators for Biological Sequence Alignment.” IEEE Transactions on Computers, Jan. 2010, vol. 59, No. 1, pp. 29-41, Washington State. [cited by applicant]
Schatz, B. Langmead, and S. Salzberg. Cloud Computing and the DNA Data Race. HHS Public Access. Published Nat Biotechnol. Jul. 2010; 28(7): 691-693. http://www.ncbi.nlm.nih.gov/pmciarticles/PMC2904649/. Retrieved May 25… [cited by applicant]
Schatz, C. Trapnell, A. Delcher, and A. Varshney. High-throughput sequence alignment using Graphics Processing Units. Published Dec. 10, 2007. BMC Bioinformatics, http://bmcbioinformatics.biomedcentral.com/; articles/10… [cited by applicant]
Schatz. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics (2009) 25 (11 ): 1363-1369. First published online: Apr. 8, 2009. http:///bioinformatics.oxfordioumals.ora/content/25/11/1363.full. Retrie… [cited by applicant]
Settle, Sean, et. al. “High-Performance Dynamic Programming on FPGAs with OpenCL.” 2013 IEEE High Performance Extreme Computing Conference {HPEC), IEEE, 2013. 6 pages. [cited by applicant]
SG Office Action in Singaporean Appln. No. 11201805562Q, dated Oct. 26, 2022, 5 pages. [cited by applicant]
Sotiriades Euripides, et al. “FPGA based Architecture for DNA Sequence Comparison and Database Search”, University of Crete, 2006, 8 pgs, Crete, Greece. [cited by applicant]
Sotiriades Euripides, et al., “Some Initial Results on Hardware BLAST acceleration with a Reconfigurable; Architecture”, University of Crete, 2006, 8 pas, Crete, Greece. [cited by applicant]
Sun, Yanteng, et. al. “Accelerating HM Mer on FPGAs Using Systolic Array Based Architecture.” IEEE International Symposium on Parallel & Distributed Processing, IEEE, 2009. 8 pages. [cited by applicant]
Tang et al., “Accelerating Millions of Short Reads Mapping on a Heterogeneous Architecture with FPGA Accelerator,” FCCM, IEEE, Apr. 29, 2012, 184-7. [cited by applicant]
TimeLogic Division, Active Motif Inc., “Accelerated BLAST Performance with Tera-Blast: a comparison of FPGA versus GPU and CPU Blast implementations”, Technical Note, May 2013, 5 pages, Version 1.0. [cited by applicant]
Treangen, T., et al., “Gapped extension for local multiple alignment of interspersed DNA repeats”, ISBRA 2008, LNBI 4983, May 7, 2007, 74-86. [cited by applicant]
Office Action in U.S. Appl. No. 15/048,935, dated Sep. 14, 2021, 21 pages. [cited by applicant]
Van Court et al., Families of FPGA-Based Algorithms for Approximate String Matching, (2004), 11 PQS, Boston University, ECE Dept., MA. [cited by applicant]
Van Der Auwera et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. HHS Public Access, Published online Oct. 15, 2013, http://www.ncbi.nlm.nih. qov/pmc/articles/P… [cited by applicant]
Wu and Colin K. Watanabe. Sequence analysis: “GMAP: a genomic mapping and alignment program for mRNA and EST sequences.” Publication Feb. 22, 2005. Bioinformatics Original Paper. vol. 21 No. 92005, pp. 1859-1875. South … [cited by applicant]
Yamaguchi, et al., High Speed Homology Search with FPGAs, Pacific Symposium On Biocomputing 7:271-282 (2002), Japan. [cited by applicant]
Yu, et al, A Smith-Waterman Systolic Cell, (2003), 10 pgs Dept. of Computer Science, The Chinese University of HonQ KonQ. [cited by applicant]
Zhang et al. A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies. PLOS One. Published: Mar. 14, 2011, http://joumals.plos.org/plosone/article?id=10.1371 / journal… [cited by applicant]
Choi et al., “A quantitative analysis on microarchitectures of modern CPU-FPGA platforms,” 53nd ACM/EDAC/IEEE Design Automation Conference (DAC), Jun. 5, 2016, 1-6. [cited by applicant]
IN Office Action in Indian Appln. No. 201827043970, dated Sep. 9, 2021, 6 pages (with English translation). [cited by applicant]
Doddavula et al., “Implementation of a Scalable Next Generation Sequencing Business Cloud Platform—An Experience Report,” Paper, Presented at the 2011 IEEE 4th International Conference on Cloud Computing, Washington D.C… [cited by applicant]
EP Office Action in European Appln. No. 17798358.2, mailed on Mar. 11, 2025, 6 pages. [cited by applicant]
EP Extended European Search Report in European Appln. No. 24162764.5, mailed on Jun. 17, 2024, 9 pages A43. [cited by applicant]
KR Office Action in Korean Appln. No. 10-2024-7005077, mailed on Dec. 12, 2024, 19 pages (with English translation). [cited by applicant]
Office Action in U.S. Appl. No. 15/616,833, mailed on Apr. 4, 2019, 6 pages. [cited by applicant]
Office Action in U.S. Appl. No. 15/643,381, mailed on Jan. 22, 2018, 9 pages. [cited by applicant]
Office Action in U.S. Appl. No. 15/907,263, mailed on May 3, 2018, 6 pages. [cited by applicant]
Office Action in U.S. Appl. No. 15/915,013, mailed on Oct. 2, 2020, 5 pages. [cited by applicant]
Office Action in U.S. Appl. No. 16/120,103, mailed on Oct. 5, 2020, 5 pages. [cited by applicant]
Wang et al., “Heterogeneous cloud framework for big data genome sequencing,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, Sep. 2014, 12(1):166-78. [cited by applicant]
AU Office Action in Australian Appln. No. 2022228089, mailed on Sep. 23, 2024, 3 pages. [cited by applicant]
AU Office Action in Australian Appln. No. 2022252718, dated Jul. 27, 2023, 3 pages. [cited by applicant]
AU Office Action in Australian Appln. No. 2022252718, mailed on Jul. 19, 2024, 3 pages. [cited by applicant]
Booth et al., “Bio-Linux as a tool for bioinformatics training,” 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE), Nov. 2012, 578-82. [cited by applicant]
BR Office Action in Brazilian appln. No. BR112018014086-4, dated Sep. 16, 2022, 8 pages (with English translation). [cited by applicant]
CA Office Action in Canadian Appln. No. 3,026,644, dated Jul. 21, 2023, 4 pages. [cited by applicant]
CA Office Action in Canadian AppIn. No. 3,008,176, dated Feb. 21, 2023, 5 pages. [cited by applicant]
CA Office Action in Canadian Appln. No. 3026644, mailed on Apr. 10, 2024, 7 pages. [cited by applicant]
CN Office Action in Chinese Appln. No. 201780035840.3, dated Sep. 5, 2022, 12 pages (with English translation). [cited by applicant]
CN Office Action in Chinese Appln. No. 201780035840.3, mailed on Aug. 9, 2023, 4 pages (with English translation). [cited by applicant]
Derrien et al., “Hardware acceleration of HMMER on FPGAs,” Journal of Signal Processing Systems, Jan. 2010, 58(1):53-67. [cited by applicant]
EP Office Action in European Appln. No. 21190670.6, dated Feb. 1, 2023, 9 pages. [cited by applicant]
Grabherr et al., “Genome-wide synteny through highly sensitive sequence alignment: Satsuma,” Bioinformatics, May 1, 2010, 26(9):1145-51. [cited by applicant]
Guo et al., “A Systolic Array-Based FPGA Parallel Architecture for the BLAST Algorithm,” International Scholarly Research Notices, Sep. 2012, vol. 2012(1):195658, 13 pages. [cited by applicant]
Hwang et al., “The mechanism of personalized service recommendation for the academic field,” 2017 4th International Conference on Computer Applications and Information Processing Technology (CAIPT), Aug. 8, 2017, 5 page… [cited by applicant]
IL Office Action in Israeli Appln. No. 263528, dated Jun. 22, 2023, 6 pages (with English translation). [cited by applicant]
IN Office Action in Indian Appln. No. 202218018463, mailed on Sep. 26, 2024, 7 pages. [cited by applicant]
IN Office Action in Indian Appln. No. 202218018469, mailed on Sep. 26, 2024, 8 pages. [cited by applicant]
Iqbal et al., “De novo assembly and genotyping of variants using colored de Bruijn graphs,” Nature Genetics, Feb. 2012, 44(2):226, 17 pages. [cited by applicant]
Jiang et al., “An efficient parallel implementation of the hidden markov methods for genomic sequence-search on a massively parallel system,” IEEE Transactions on Parallel and Distributed Systems, Dec. 2007, 19(1):15-23. [cited by applicant]
JP Japanese Office Action in Japanese Appln. No. 2022-046805, dated Jun. 5, 2023, 18 pages (with English translation). [cited by applicant]
JP Notice of Allowance in Japanese Appln. No. 2018-555440, dated Jun. 12, 2023, 6 pages (with English translation). [cited by applicant]
JP Office Action in Japanese Appln. No. 2022-089149, dated Jun. 19, 2023, 9 pages (with English translation). [cited by applicant]
Luethy et al., “Hardware and software systems for accelerating common bioinformatics sequence analysis algorithms,” Drug Discovery Today: BIOSILICO, Jan. 2004, 2(1):12-7. [cited by applicant]
Mandelker et al., “Navigating highly homologous genes in a molecular diagnostic setting: a resource for clinical next-generation sequencing,” Genetics in Medicine, Dec. 2016, 18(12):1282-9. [cited by applicant]
ML Office Action in Malaysian Appln. No. PI 2018702376, dated Jun. 17, 2022, 3 pages. [cited by applicant]
MX Office Action in Mexican Appln. No. MX/a/2018/008527, dated May 25, 2023, 9 pages (with English translation). [cited by applicant]
Notice of Acceptance in South African Appln. No. 2022/10297, dated Jun. 5, 2023, 2 pages. [cited by applicant]
NZ Office Action in New Zealand Appln. No. 748612, mailed on Dec. 15, 2023, 3 pages. [cited by applicant]
NZ Office Action in New Zealand Appln. No. 789137, mailed on Mar. 5, 2024, 2 pages. [cited by applicant]
NZ Office Action in New Zealand Appln. No. 789138, mailed on Mar. 13, 2024, 2 pages. [cited by applicant]
Office Action in New Zealand Appln. No. 743311, dated Jun. 21, 2023, 3 pages. [cited by applicant]
Office Action in New Zealand Appln. No. 784186, dated Jun. 29, 2023, 3 pages. [cited by applicant]
Office Action in New Zealand Appln. No. 784189, dated Jun. 27, 2023, 3 pages. [cited by applicant]
Oliver et al., “High performance database searching with HMMer on FPGAs,” 2007 IEEE International Parallel and Distributed Processing Symposium, Mar. 26, 2007, 7 pages. [cited by applicant]
RU Office Action in Russian Appln. No. 2021118824, dated Oct. 17, 2022, 21 pages (with English translation). [cited by applicant]
Wilke et al., “A RESTful API for accessing microbial community data for MG-RAST,” PLoS Computational Biology, Jan. 8, 2015, 11(1):e1004008, 8 pages. [cited by applicant]
Zhang et al., “Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads,” Bioinformatics, Oct. 2013, 29(19):2427-34. [cited by applicant]