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Improved base calling for the Illumina Genome Analyzer using machine learning strategies.

Kircher M, Stenzel U, Kelso J.

Genome Biol. 2009;10(8):R83. doi: 10.1186/gb-2009-10-8-r83. Epub 2009 Aug 14.


leeHom: adaptor trimming and merging for Illumina sequencing reads.

Renaud G, Stenzel U, Kelso J.

Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.


freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers.

Renaud G, Kircher M, Stenzel U, Kelso J.

Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.


deML: robust demultiplexing of Illumina sequences using a likelihood-based approach.

Renaud G, Stenzel U, Maricic T, Wiebe V, Kelso J.

Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.


Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.

Erlich Y, Mitra PP, delaBastide M, McCombie WR, Hannon GJ.

Nat Methods. 2008 Aug;5(8):679-82. doi: 10.1038/nmeth.1230. Epub 2008 Jul 6.


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.


OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing.

Das S, Vikalo H.

Bioinformatics. 2012 Jul 1;28(13):1677-83. doi: 10.1093/bioinformatics/bts256. Epub 2012 May 7.


pIRS: Profile-based Illumina pair-end reads simulator.

Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Y, Mu D, Zhang H, Li N, Yue Z, Bai F, Li H, Fan W.

Bioinformatics. 2012 Jun 1;28(11):1533-5. doi: 10.1093/bioinformatics/bts187. Epub 2012 Apr 15.


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.


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.


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.


Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads.

Duitama J, Kennedy J, Dinakar S, Hernández Y, Wu Y, Măndoiu II.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S53. doi: 10.1186/1471-2105-12-S1-S53.


FastUniq: a fast de novo duplicates removal tool for paired short reads.

Xu H, Luo X, Qian J, Pang X, Song J, Qian G, Chen J, Chen S.

PLoS One. 2012;7(12):e52249. doi: 10.1371/journal.pone.0052249. Epub 2012 Dec 20.


Probabilistic base calling of Solexa sequencing data.

Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F.

BMC Bioinformatics. 2008 Oct 13;9:431. doi: 10.1186/1471-2105-9-431.


SlideSort: all pairs similarity search for short reads.

Shimizu K, Tsuda K.

Bioinformatics. 2011 Feb 15;27(4):464-70. doi: 10.1093/bioinformatics/btq677. Epub 2010 Dec 9.


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.


Base calling for high-throughput short-read sequencing: dynamic programming solutions.

Das S, Vikalo H.

BMC Bioinformatics. 2013 Apr 15;14:129. doi: 10.1186/1471-2105-14-129.


De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads.

Farrer RA, Kemen E, Jones JD, Studholme DJ.

FEMS Microbiol Lett. 2009 Feb;291(1):103-11. doi: 10.1111/j.1574-6968.2008.01441.x. Epub 2008 Dec 9.


BSMAP: whole genome bisulfite sequence MAPping program.

Xi Y, Li W.

BMC Bioinformatics. 2009 Jul 27;10:232. doi: 10.1186/1471-2105-10-232.


Base-calling of automated sequencer traces using phred. I. Accuracy assessment.

Ewing B, Hillier L, Wendl MC, Green P.

Genome Res. 1998 Mar;8(3):175-85.

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