Sequence assembly

1. A method for assembling and aligning a plurality of sequence reads having mutations of different types, the method comprising:

obtaining a sample comprising a template nucleic acid;

sequencing the sample to generate the plurality of sequence reads, the sequencing comprising;

fragmenting the template nucleic acid,

attaching the fragments to a surface of channels in a flow cell, and

amplifying the attached fragments to create clusters, each cluster comprising a plurality of copies of the template nucleic acid in one of the channels in the flow cell;

inputting a reference genome and the plurality of sequence reads into a computer system comprising a non-transitory memory and a processor coupled to the non-transitory memory, wherein the non-transitory memory has instructions stored thereon that, when executed by the processor, cause the processor to perform the steps of:

assembling a contig from at least some of the plurality of sequence reads;

identifying a plurality of contig-to-reference descriptions of the mutations by aligning the contig to a sequence of the reference genome, the mutations including a substitution and an indel;

identifying a plurality of read-to-contig descriptions by aligning each of the at least some of the plurality of sequence reads to the contig; and

generating a read-to-reference description by aligning at least one of the plurality of contig-to-reference descriptions with a corresponding at least one of the plurality of read-to-contig descriptions, wherein the read-to-reference description maps positional information of the mutations found in at least one of the at least some of the plurality of sequence reads relative to the sequence of the reference genome.

2. The method of claim 1 , further comprising attaching a barcode sequence to the template nucleic acid.

3. The method of claim 2 , further comprising assigning one of the plurality of sequence reads to a subset based on the barcode sequence.

4. The method of claim 3 , wherein the subset is used to create a unique contig for the subset.

5. The method of claim 1 , wherein assembling the contig comprises overlap consensus assembly.

6. The method of claim 1 , wherein assembling the contig comprises searching a prefix tree for overlap between the plurality of sequence reads.

7. The method of claim 1 , further comprising identifying the mutations based on one or more alignments between the contig and the sequence of the reference genome.

8. The method of claim 1 , wherein the substitution is within 100 nucleotides of the indel.

9. The method of claim 1 , wherein the sequencing comprises sequencing-by-synthesis.

10. The method of claim 1 , wherein aligning the contig to the sequence of the reference genome is performed using a first plurality of alignment parameters and aligning each of the at least some of the plurality of sequence reads to the contig is performed using a second plurality of alignment parameters.

11. The method of claim 10 , wherein the first plurality of alignment parameters includes a first gap penalty and a first substitution probability, the second plurality of alignment parameters includes a second gap penalty and a second substitution probability, and the first gap penalty is greater than the second gap penalty.

12. The method of claim 1 , wherein the template nucleic acid is DNA or RNA.

13. The method of claim 12 , wherein the template nucleic acid is tumor DNA.

14. The method of claim 12 , wherein the template nucleic acid is circulating fetal DNA.

15. The method of claim 1 , wherein the reference genome is a human genome.

16. The method of claim 1 , wherein the instructions further cause the processor to create a file or variable containing a description of the mutations.

17. The method of claim 16 , wherein the file or variable is a binary alignment map (BAM) file comprising a Compact Idiosyncratic Gapped Alignment Report (CIGAR) string.

18. The method of claim 16 , wherein the description of the mutations comprises variant and positional information.