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Items: 1 to 20 of 251

1.

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.

PMID:
22689389
2.

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.

3.

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
4.

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.

5.

Long read alignment based on maximal exact match seeds.

Liu Y, Schmidt B.

Bioinformatics. 2012 Sep 15;28(18):i318-i324. doi: 10.1093/bioinformatics/bts414.

6.

BS Seeker: precise mapping for bisulfite sequencing.

Chen PY, Cokus SJ, Pellegrini M.

BMC Bioinformatics. 2010 Apr 23;11:203. doi: 10.1186/1471-2105-11-203.

7.

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.

PMID:
23267171
8.

Short Read Alignment Using SOAP2.

Hurgobin B.

Methods Mol Biol. 2016;1374:241-52. doi: 10.1007/978-1-4939-3167-5_13.

PMID:
26519410
9.

MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.

Turki T, Roshan U.

BMC Genomics. 2014 Nov 15;15:969. doi: 10.1186/1471-2164-15-969.

10.

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.

Chen Y, Souaiaia T, Chen T.

Bioinformatics. 2009 Oct 1;25(19):2514-21. doi: 10.1093/bioinformatics/btp486. Epub 2009 Aug 12.

11.

Short read alignment with populations of genomes.

Huang L, Popic V, Batzoglou S.

Bioinformatics. 2013 Jul 1;29(13):i361-70. doi: 10.1093/bioinformatics/btt215.

12.

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.

13.

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.

Kim YJ, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM.

Bioinformatics. 2009 Jun 1;25(11):1424-5. doi: 10.1093/bioinformatics/btp178. Epub 2009 Apr 7.

14.

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.

15.

Fast inexact mapping using advanced tree exploration on backward search methods.

Salavert J, Tomás A, Tárraga J, Medina I, Dopazo J, Blanquer I.

BMC Bioinformatics. 2015 Jan 28;16:18. doi: 10.1186/s12859-014-0438-3.

16.

YOABS: yet other aligner of biological sequences--an efficient linearly scaling nucleotide aligner.

Galinsky VL.

Bioinformatics. 2012 Apr 15;28(8):1070-7. doi: 10.1093/bioinformatics/bts102. Epub 2012 Mar 7.

PMID:
22402614
17.

Blue: correcting sequencing errors using consensus and context.

Greenfield P, Duesing K, Papanicolaou A, Bauer DC.

Bioinformatics. 2014 Oct;30(19):2723-32. doi: 10.1093/bioinformatics/btu368. Epub 2014 Jun 11.

PMID:
24919879
18.

ARYANA: Aligning Reads by Yet Another Approach.

Gholami M, Arbabi A, Sharifi-Zarchi A, Chitsaz H, Sadeghi M.

BMC Bioinformatics. 2014;15 Suppl 9:S12. doi: 10.1186/1471-2105-15-S9-S12. Epub 2014 Sep 10.

19.

BOAT: Basic Oligonucleotide Alignment Tool.

Zhao SQ, Wang J, Zhang L, Li JT, Gu X, Gao G, Wei L.

BMC Genomics. 2009 Dec 3;10 Suppl 3:S2. doi: 10.1186/1471-2164-10-S3-S2.

20.

libgapmis: extending short-read alignments.

Alachiotis N, Berger S, Flouri T, Pissis SP, Stamatakis A.

BMC Bioinformatics. 2013;14 Suppl 11:S4. doi: 10.1186/1471-2105-14-S11-S4. Epub 2013 Nov 4.

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