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Results: 1 to 20 of 141

1.

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA.

Homer N, Nelson SF.

Genome Biol. 2010;11(10):R99. doi: 10.1186/gb-2010-11-10-r99. Epub 2010 Oct 8.

PMID:
20932289
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Analysis of high-throughput sequencing data.

Mane SP, Modise T, Sobral BW.

Methods Mol Biol. 2011;678:1-11. doi: 10.1007/978-1-60761-682-5_1.

PMID:
20931368
[PubMed - indexed for MEDLINE]
3.

Comparison of solution-based exome capture methods for next generation sequencing.

Sulonen AM, Ellonen P, Almusa H, Lepistö M, Eldfors S, Hannula S, Miettinen T, Tyynismaa H, Salo P, Heckman C, Joensuu H, Raivio T, Suomalainen A, Saarela J.

Genome Biol. 2011 Sep 28;12(9):R94. doi: 10.1186/gb-2011-12-9-r94.

PMID:
21955854
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome.

Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JD, Varshney RK.

Am J Bot. 2012 Feb;99(2):186-92. doi: 10.3732/ajb.1100419. Epub 2012 Feb 1.

PMID:
22301893
[PubMed - indexed for MEDLINE]
Free Article
5.

A survey of sequence alignment algorithms for next-generation sequencing.

Li H, Homer N.

Brief Bioinform. 2010 Sep;11(5):473-83. doi: 10.1093/bib/bbq015. Epub 2010 May 11. Review.

PMID:
20460430
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.

Rausch T, Koren S, Denisov G, Weese D, Emde AK, Döring A, Reinert K.

Bioinformatics. 2009 May 1;25(9):1118-24. doi: 10.1093/bioinformatics/btp131. Epub 2009 Mar 5.

PMID:
19269990
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Ψ-RA: a parallel sparse index for genomic read alignment.

Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B.

BMC Genomics. 2011;12 Suppl 2:S7. doi: 10.1186/1471-2164-12-S2-S7. Epub 2011 Jul 27.

PMID:
21989248
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

SOAP2: an improved ultrafast tool for short read alignment.

Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J.

Bioinformatics. 2009 Aug 1;25(15):1966-7. doi: 10.1093/bioinformatics/btp336. Epub 2009 Jun 3.

PMID:
19497933
[PubMed - indexed for MEDLINE]
Free Article
9.

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
10.

The Sequence Alignment/Map format and SAMtools.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup.

Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.

PMID:
19505943
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Computational methods for discovering structural variation with next-generation sequencing.

Medvedev P, Stanciu M, Brudno M.

Nat Methods. 2009 Nov;6(11 Suppl):S13-20. doi: 10.1038/nmeth.1374. Review.

PMID:
19844226
[PubMed - indexed for MEDLINE]
12.

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory.

Chaisson MJ, Tesler G.

BMC Bioinformatics. 2012 Sep 19;13:238. doi: 10.1186/1471-2105-13-238.

PMID:
22988817
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

CloudBurst: highly sensitive read mapping with MapReduce.

Schatz MC.

Bioinformatics. 2009 Jun 1;25(11):1363-9. doi: 10.1093/bioinformatics/btp236. Epub 2009 Apr 8.

PMID:
19357099
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming.

Blom J, Jakobi T, Doppmeier D, Jaenicke S, Kalinowski J, Stoye J, Goesmann A.

Bioinformatics. 2011 May 15;27(10):1351-8. doi: 10.1093/bioinformatics/btr151. Epub 2011 Mar 30.

PMID:
21450712
[PubMed - indexed for MEDLINE]
Free Article
15.

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.

Bioinformatics. 2010 Mar 15;26(6):730-6. doi: 10.1093/bioinformatics/btq040. Epub 2010 Feb 3.

PMID:
20130035
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.

McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP.

Genome Res. 2009 Sep;19(9):1527-41. doi: 10.1101/gr.091868.109. Epub 2009 Jun 22.

PMID:
19546169
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Short read DNA fragment anchoring algorithm.

Wang W, Zhang P, Liu X.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S17. doi: 10.1186/1471-2105-10-S1-S17.

PMID:
19208116
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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
19.

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing.

Qu W, Hashimoto S, Morishita S.

Genome Res. 2009 Jul;19(7):1309-15. doi: 10.1101/gr.089151.108. Epub 2009 May 13.

PMID:
19439514
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

De novo fragment assembly with short mate-paired reads: Does the read length matter?

Chaisson MJ, Brinza D, Pevzner PA.

Genome Res. 2009 Feb;19(2):336-46. doi: 10.1101/gr.079053.108. Epub 2008 Dec 3.

PMID:
19056694
[PubMed - indexed for MEDLINE]
Free PMC Article

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