GENOME ASSEMBLY
The invention generally relates to methods for assembling sequence contigs. In certain embodiments, methods of the invention involve converting sequence contigs into maps, generating a plurality of single molecule restriction maps, aligning single molecule restriction maps to ends of the maps of the sequence contigs, thereby producing extended sequence contigs, and aligning extended sequence contigs.
1 . A method for assembling sequence contigs, the method comprising:
converting sequence contigs into maps;
generating a plurality of single molecule restriction maps;
aligning single molecule restriction maps to ends of the maps of the sequence contigs, thereby producing extended sequence contigs; and
aligning extended sequence contigs.
2 . The method according to claim 1 , wherein generating comprises:
introducing the nucleic acids to a charged substrate so that the nucleic acids become elongated and fixed on the subject in a manner in which the nucleic acids remain accessible for enzymatic reactions;
digesting the nucleic acids enzymatically to produce one or more restriction digests; and
constructing a map from the restriction digests.
3 . The method according to claim 2 , wherein the substrate is derivatized glass.
4 . The method according to claim 3 , wherein the glass is derivatized with silanes.
5 . The method according to claim 1 , wherein the sample is a human tissue or body fluid.
6 . The method according to claim 1 , wherein the sample is from a microorganism.
7 . The method according to claim 6 , wherein the microorganism is a selected from the group consisting of a bacterium, a fungus, and a virus.
8 . The method according to claim 1 , further comprising determining contig arrangement.
9 . The method according to claim 1 , further comprising determining contig orientation.
10 . The method according to claim 1 , further comprising identifying assembly errors in the sequence contigs.
11 . The method according to claim 1 , wherein the nucleic acids are several hundred kilobases in length.
12 . The method according to claim 1 , wherein the single molecule restriction maps span gaps between the sequence contigs.
13 . A method for assembling sequence contigs, the method comprising:
using mapping to generate single molecule restriction maps;
extending sequence reads by aligning single molecule restriction maps to ends of maps of sequence contigs, thereby producing extended sequence contigs; and
aligning the extended sequence contigs.
14 . The method according to claim 13 , wherein generating comprises:
introducing the nucleic acids to a charged substrate so that the nucleic acids become elongated and fixed on the subject in a manner in which the nucleic acids remain accessible for enzymatic reactions;
digesting the nucleic acids enzymatically to produce one or more restriction digests; and
constructing a map from the restriction digests.
15 . The method according to claim 14 , wherein the substrate is derivatized glass.
16 . The method according to claim 15 , wherein the glass is derivatized with silanes.
17 . The method according to claim 14 , wherein the sample is a human tissue or body fluid.
18 . The method according to claim 14 , wherein the sample is from a microorganism.
19 . The method according to claim 18 , wherein the microorganism is a selected from the group consisting of a bacterium, a fungus, and a virus.
20 . The method according to claim 14 , further comprising determining contig arrangement.
21 . The method according to claim 14 , further comprising determining contig orientation.
22 . The method according to claim 14 , further comprising identifying assembly errors in the sequence contigs.
23 . The method according to claim 14 , wherein the single molecule restriction maps span gaps between the sequence contigs.