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Items: 1 to 20 of 97

1.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

2.

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.

3.

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.

4.

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
5.

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
6.

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.

7.

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
8.

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
9.

Aligning short sequencing reads with Bowtie.

Langmead B.

Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.7. doi: 10.1002/0471250953.bi1107s32.

10.

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.

Liu CM, Wong T, Wu E, Luo R, Yiu SM, Li Y, Wang B, Yu C, Chu X, Zhao K, Li R, Lam TW.

Bioinformatics. 2012 Mar 15;28(6):878-9. doi: 10.1093/bioinformatics/bts061. Epub 2012 Jan 28.

PMID:
22285832
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.

Faster single-end alignment generation utilizing multi-thread for BWA.

Jo H, Koh G.

Biomed Mater Eng. 2015;26 Suppl 1:S1791-6. doi: 10.3233/BME-151480.

PMID:
26405948
13.

CLAST: CUDA implemented large-scale alignment search tool.

Yano M, Mori H, Akiyama Y, Yamada T, Kurokawa K.

BMC Bioinformatics. 2014 Dec 11;15:406. doi: 10.1186/s12859-014-0406-y.

14.

FANSe2: a robust and cost-efficient alignment tool for quantitative next-generation sequencing applications.

Xiao CL, Mai ZB, Lian XL, Zhong JY, Jin JJ, He QY, Zhang G.

PLoS One. 2014 Apr 17;9(4):e94250. doi: 10.1371/journal.pone.0094250. eCollection 2014.

15.

Fast gapped-read alignment with Bowtie 2.

Langmead B, Salzberg SL.

Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.

16.

HISAT: a fast spliced aligner with low memory requirements.

Kim D, Langmead B, Salzberg SL.

Nat Methods. 2015 Apr;12(4):357-60. doi: 10.1038/nmeth.3317. Epub 2015 Mar 9.

17.

TotalReCaller: improved accuracy and performance via integrated alignment and base-calling.

Menges F, Narzisi G, Mishra B.

Bioinformatics. 2011 Sep 1;27(17):2330-7. doi: 10.1093/bioinformatics/btr393. Epub 2011 Jun 30.

PMID:
21724593
18.

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.

19.

Multi-threading the generation of Burrows-Wheeler Alignment.

Jo H.

Genet Mol Res. 2016 May 23;15(2). doi: 10.4238/gmr.15028650.

20.

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.

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