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Results: 1 to 20 of 104

1.

Quake: quality-aware detection and correction of sequencing errors.

Kelley DR, Schatz MC, Salzberg SL.

Genome Biol. 2010;11(11):R116. doi: 10.1186/gb-2010-11-11-r116. Epub 2010 Nov 29.

PMID:
21114842
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Updates to the RMAP short-read mapping software.

Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ.

Bioinformatics. 2009 Nov 1;25(21):2841-2. doi: 10.1093/bioinformatics/btp533. Epub 2009 Sep 7.

PMID:
19736251
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.

Marçais G, Kingsford C.

Bioinformatics. 2011 Mar 15;27(6):764-70. doi: 10.1093/bioinformatics/btr011. Epub 2011 Jan 7.

PMID:
21217122
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Repeat-aware modeling and correction of short read errors.

Yang X, Aluru S, Dorman KS.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S52. doi: 10.1186/1471-2105-12-S1-S52.

PMID:
21342585
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

SEQuel: improving the accuracy of genome assemblies.

Ronen R, Boucher C, Chitsaz H, Pevzner P.

Bioinformatics. 2012 Jun 15;28(12):i188-96. doi: 10.1093/bioinformatics/bts219.

PMID:
22689760
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Correction of sequencing errors in a mixed set of reads.

Salmela L.

Bioinformatics. 2010 May 15;26(10):1284-90. doi: 10.1093/bioinformatics/btq151. Epub 2010 Apr 8.

PMID:
20378555
[PubMed - indexed for MEDLINE]
Free Article
7.

Gossamer--a resource-efficient de novo assembler.

Conway T, Wazny J, Bromage A, Zobel J, Beresford-Smith B.

Bioinformatics. 2012 Jul 15;28(14):1937-8. doi: 10.1093/bioinformatics/bts297. Epub 2012 May 18.

PMID:
22611131
[PubMed - indexed for MEDLINE]
Free Article
8.

PineSAP--sequence alignment and SNP identification pipeline.

Wegrzyn JL, Lee JM, Liechty J, Neale DB.

Bioinformatics. 2009 Oct 1;25(19):2609-10. doi: 10.1093/bioinformatics/btp477. Epub 2009 Aug 10.

PMID:
19667082
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Li H, Ruan J, Durbin R.

Genome Res. 2008 Nov;18(11):1851-8. doi: 10.1101/gr.078212.108. Epub 2008 Aug 19.

PMID:
18714091
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

EagleView: a genome assembly viewer for next-generation sequencing technologies.

Huang W, Marth G.

Genome Res. 2008 Sep;18(9):1538-43. doi: 10.1101/gr.076067.108. Epub 2008 Jun 11.

PMID:
18550804
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

SNP detection for massively parallel whole-genome resequencing.

Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J.

Genome Res. 2009 Jun;19(6):1124-32. doi: 10.1101/gr.088013.108. Epub 2009 May 6.

PMID:
19420381
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A probabilistic method for the detection and genotyping of small indels from population-scale sequence data.

Bansal V, Libiger O.

Bioinformatics. 2011 Aug 1;27(15):2047-53. doi: 10.1093/bioinformatics/btr344. Epub 2011 Jun 7.

PMID:
21653520
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Scaffolding and validation of bacterial genome assemblies using optical restriction maps.

Nagarajan N, Read TD, Pop M.

Bioinformatics. 2008 May 15;24(10):1229-35. doi: 10.1093/bioinformatics/btn102. Epub 2008 Mar 20.

PMID:
18356192
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

BFAST: an alignment tool for large scale genome resequencing.

Homer N, Merriman B, Nelson SF.

PLoS One. 2009 Nov 11;4(11):e7767. doi: 10.1371/journal.pone.0007767.

PMID:
19907642
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform.

Liu Y, Schmidt B, Maskell DL.

Bioinformatics. 2012 Jul 15;28(14):1830-7. doi: 10.1093/bioinformatics/bts276. Epub 2012 May 9.

PMID:
22576173
[PubMed - indexed for MEDLINE]
Free Article
16.

Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads.

Duitama J, Kennedy J, Dinakar S, Hernández Y, Wu Y, Măndoiu II.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S53. doi: 10.1186/1471-2105-12-S1-S53.

PMID:
21342586
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

ABySS: a parallel assembler for short read sequence data.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.

Genome Res. 2009 Jun;19(6):1117-23. doi: 10.1101/gr.089532.108. Epub 2009 Feb 27.

PMID:
19251739
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data.

Zeng F, Jiang R, Chen T.

Nucleic Acids Res. 2013 Jul;41(13):e136. doi: 10.1093/nar/gkt372. Epub 2013 May 21.

PMID:
23700313
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware.

Shi H, Schmidt B, Liu W, Müller-Wittig W.

J Comput Biol. 2010 Apr;17(4):603-15. doi: 10.1089/cmb.2009.0062.

PMID:
20426693
[PubMed - indexed for MEDLINE]
20.

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.

Boisvert S, Laviolette F, Corbeil J.

J Comput Biol. 2010 Nov;17(11):1519-33. doi: 10.1089/cmb.2009.0238. Epub 2010 Oct 20.

PMID:
20958248
[PubMed - indexed for MEDLINE]
Free PMC Article

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