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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.


Fast and accurate short read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.


Fast and accurate read alignment for resequencing.

Mu JC, Jiang H, Kiani A, Mohiyuddin M, Bani Asadi N, Wong WH.

Bioinformatics. 2012 Sep 15;28(18):2366-73. doi: 10.1093/bioinformatics/bts450. Epub 2012 Jul 18.


CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.

Liu Y, Popp B, Schmidt B.

PLoS One. 2014 Jan 22;9(1):e86869. doi: 10.1371/journal.pone.0086869. eCollection 2014.


Fast and accurate long-read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2010 Mar 1;26(5):589-95. doi: 10.1093/bioinformatics/btp698. Epub 2010 Jan 15.


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.


Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC+.

González-Domínguez J, Liu Y, Schmidt B.

PLoS One. 2016 Jan 5;11(1):e0145490. doi: 10.1371/journal.pone.0145490. eCollection 2016.


SRmapper: a fast and sensitive genome-hashing alignment tool.

Gontarz PM, Berger J, Wong CF.

Bioinformatics. 2013 Feb 1;29(3):316-21. doi: 10.1093/bioinformatics/bts712. Epub 2012 Dec 24.


A hybrid short read mapping accelerator.

Chen Y, Schmidt B, Maskell DL.

BMC Bioinformatics. 2013 Feb 26;14:67. doi: 10.1186/1471-2105-14-67.


A novel partial sequence alignment tool for finding large deletions.

Aruk T, Ustek D, Kursun O.

ScientificWorldJournal. 2012;2012:694813. doi: 10.1100/2012/694813. Epub 2012 Apr 1.


GASSST: global alignment short sequence search tool.

Rizk G, Lavenier D.

Bioinformatics. 2010 Oct 15;26(20):2534-40. doi: 10.1093/bioinformatics/btq485. Epub 2010 Aug 24.


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.


Efficient alignment of pyrosequencing reads for re-sequencing applications.

Fernandes F, da Fonseca PG, Russo LM, Oliveira AL, Freitas AT.

BMC Bioinformatics. 2011 May 16;12:163. doi: 10.1186/1471-2105-12-163.


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.


Hobbes: optimized gram-based methods for efficient read alignment.

Ahmadi A, Behm A, Honnalli N, Li C, Weng L, Xie X.

Nucleic Acids Res. 2012 Mar;40(6):e41. doi: 10.1093/nar/gkr1246. Epub 2011 Dec 22.


BatMis: a fast algorithm for k-mismatch mapping.

Tennakoon C, Purbojati RW, Sung WK.

Bioinformatics. 2012 Aug 15;28(16):2122-8. doi: 10.1093/bioinformatics/bts339. Epub 2012 Jun 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.


Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.

Hong C, Clement NL, Clement S, Hammoud SS, Carrell DT, Cairns BR, Snell Q, Clement MJ, Johnson WE.

BMC Bioinformatics. 2013 Nov 21;14:337. doi: 10.1186/1471-2105-14-337.


SAP--a sequence mapping and analyzing program for long sequence reads alignment and accurate variants discovery.

Sun Z, Tian W.

PLoS One. 2012;7(8):e42887. doi: 10.1371/journal.pone.0042887. Epub 2012 Aug 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.

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