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Items: 1 to 20 of 235

1.

SHRiMP: accurate mapping of short color-space reads.

Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M.

PLoS Comput Biol. 2009 May;5(5):e1000386. doi: 10.1371/journal.pcbi.1000386. Epub 2009 May 22.

2.

SHRiMP2: sensitive yet practical SHort Read Mapping.

David M, Dzamba M, Lister D, Ilie L, Brudno M.

Bioinformatics. 2011 Apr 1;27(7):1011-2. doi: 10.1093/bioinformatics/btr046. Epub 2011 Jan 28.

PMID:
21278192
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.

ComB: SNP calling and mapping analysis for color and nucleotide space platforms.

Souaiaia T, Frazier Z, Chen T.

J Comput Biol. 2011 Jun;18(6):795-807. doi: 10.1089/cmb.2011.0027. Epub 2011 May 12.

5.

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.

6.

Incorporating sequence quality data into alignment improves DNA read mapping.

Frith MC, Wan R, Horton P.

Nucleic Acids Res. 2010 Apr;38(7):e100. doi: 10.1093/nar/gkq010. Epub 2010 Jan 27.

7.

Optimal spliced alignments of short sequence reads.

De Bona F, Ossowski S, Schneeberger K, Rätsch G.

Bioinformatics. 2008 Aug 15;24(16):i174-80. doi: 10.1093/bioinformatics/btn300.

PMID:
18689821
8.

VARiD: a variation detection framework for color-space and letter-space platforms.

Dalca AV, Rumble SM, Levy S, Brudno M.

Bioinformatics. 2010 Jun 15;26(12):i343-9. doi: 10.1093/bioinformatics/btq184.

9.

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.

10.

MOM: maximum oligonucleotide mapping.

Eaves HL, Gao Y.

Bioinformatics. 2009 Apr 1;25(7):969-70. doi: 10.1093/bioinformatics/btp092. Epub 2009 Feb 19.

PMID:
19228804
11.

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.

PMID:
21856737
12.

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.

13.

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.

14.

RazerS--fast read mapping with sensitivity control.

Weese D, Emde AK, Rausch T, Döring A, Reinert K.

Genome Res. 2009 Sep;19(9):1646-54. doi: 10.1101/gr.088823.108. Epub 2009 Jul 10.

15.

Using quality scores and longer reads improves accuracy of Solexa read mapping.

Smith AD, Xuan Z, Zhang MQ.

BMC Bioinformatics. 2008 Feb 28;9:128. doi: 10.1186/1471-2105-9-128.

16.

An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome.

Shrestha AM, Frith MC.

Bioinformatics. 2013 Apr 15;29(8):965-72. doi: 10.1093/bioinformatics/btt073. Epub 2013 Feb 14.

17.

Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.

Misra S, Agrawal A, Liao WK, Choudhary A.

Bioinformatics. 2011 Jan 15;27(2):189-95. doi: 10.1093/bioinformatics/btq648. Epub 2010 Nov 18.

PMID:
21088030
18.

Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis.

Schbath S, Martin V, Zytnicki M, Fayolle J, Loux V, Gibrat JF.

J Comput Biol. 2012 Jun;19(6):796-813. doi: 10.1089/cmb.2012.0022. Epub 2012 Apr 16.

19.

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.

20.

Fragment assembly with short reads.

Chaisson M, Pevzner P, Tang H.

Bioinformatics. 2004 Sep 1;20(13):2067-74. Epub 2004 Apr 1.

PMID:
15059830

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