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Items: 1 to 20 of 304


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.


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.


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.


Comparative analysis of algorithms for next-generation sequencing read alignment.

Ruffalo M, LaFramboise T, Koyutürk M.

Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477. Epub 2011 Aug 19.


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.


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 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.


Accurate estimation of short read mapping quality for next-generation genome sequencing.

Ruffalo M, Koyutürk M, Ray S, LaFramboise T.

Bioinformatics. 2012 Sep 15;28(18):i349-i355. doi: 10.1093/bioinformatics/bts408.


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.


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.


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.


A random-permutations-based approach to fast read alignment.

Lederman R.

BMC Bioinformatics. 2013;14 Suppl 5:S8. doi: 10.1186/1471-2105-14-S5-S8. Epub 2013 Apr 10.


The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote.

Liao Y, Smyth GK, Shi W.

Nucleic Acids Res. 2013 May 1;41(10):e108. doi: 10.1093/nar/gkt214. Epub 2013 Apr 4.


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.


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.


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.


Re-alignment of the unmapped reads with base quality score.

Peng X, Wang J, Zhang Z, Xiao Q, Li M, Pan Y.

BMC Bioinformatics. 2015;16 Suppl 5:S8. doi: 10.1186/1471-2105-16-S5-S8. Epub 2015 Mar 18.


SCALCE: boosting sequence compression algorithms using locally consistent encoding.

Hach F, Numanagic I, Alkan C, Sahinalp SC.

Bioinformatics. 2012 Dec 1;28(23):3051-7. doi: 10.1093/bioinformatics/bts593. Epub 2012 Oct 9.


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.


Identification of indels in next-generation sequencing data.

Ratan A, Olson TL, Loughran TP Jr, Miller W.

BMC Bioinformatics. 2015 Feb 13;16:42. doi: 10.1186/s12859-015-0483-6.

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