PubMed

Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data.

Parker NJ, Parker AG.

Source Code Biol Med. 2008 Apr 18;3:5.PMID: 18423012 [PubMed - in process]Related articlesFree article

Whole-genome sequencing and assembly with high-throughput, short-read technologies.

Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S.

PLoS One. 2007 May 30;2(5):e484.PMID: 17534434 [PubMed - in process]Related articlesFree article

Comparison of next generation sequencing technologies for transcriptome characterization.

Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster SC, Soltis DE, Soltis PS, Altman N, dePamphilis CW.

BMC Genomics. 2009 Aug 1;10:347.PMID: 19646272 [PubMed - indexed for MEDLINE]Related articlesFree article

Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.

Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS.

BMC Genomics. 2008 Aug 28;9:404.PMID: 18755037 [PubMed - indexed for MEDLINE]Related articlesFree article

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing.

Qu W, Hashimoto S, Morishita S.

Genome Res. 2009 Jul;19(7):1309-15. Epub 2009 May 13.PMID: 19439514 [PubMed - indexed for MEDLINE]Related articlesFree article

SHREC: a short-read error correction method.

Schröder J, Schröder H, Puglisi SJ, Sinha R, Schmidt B.

Bioinformatics. 2009 Sep 1;25(17):2157-63. Epub 2009 Jun 19.PMID: 19542152 [PubMed - indexed for MEDLINE]Related articles

STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.

Kraemer L, Beszteri B, Gäbler-Schwarz S, Held C, Leese F, Mayer C, Pöhlmann K, Frickenhaus S.

BMC Bioinformatics. 2009 Jan 30;10:41.PMID: 19183437 [PubMed - indexed for MEDLINE]Related articlesFree article

The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing.

Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, Hekele A, DeRisi JL.

PLoS One. 2008;3(10):e3495. Epub 2008 Oct 22.PMID: 18941527 [PubMed - indexed for MEDLINE]Related articlesFree article

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.

Rausch T, Koren S, Denisov G, Weese D, Emde AK, Döring A, Reinert K.

Bioinformatics. 2009 May 1;25(9):1118-24. Epub 2009 Mar 5.PMID: 19269990 [PubMed - indexed for MEDLINE]Related articles

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.

Dohm JC, Lottaz C, Borodina T, Himmelbauer H.

Nucleic Acids Res. 2008 Sep;36(16):e105. Epub 2008 Jul 26.PMID: 18660515 [PubMed - indexed for MEDLINE]Related articlesFree article

A fast hybrid short read fragment assembly algorithm.

Schmidt B, Sinha R, Beresford-Smith B, Puglisi SJ.

Bioinformatics. 2009 Sep 1;25(17):2279-80. Epub 2009 Jun 17.PMID: 19535537 [PubMed - indexed for MEDLINE]Related articles

EnGenIUS -- Environmental Genome Informational Utility System.

Kaplarevic M, Murray AE, Cary SC, Gao GR.

J Bioinform Comput Biol. 2008 Dec;6(6):1193-211.PMID: 19090024 [PubMed - indexed for MEDLINE]Related articles

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB.

PLoS Comput Biol. 2009 Jul;5(7):e1000432. Epub 2009 Jul 10.PMID: 19593373 [PubMed - indexed for MEDLINE]Related articlesFree article

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.

Schreiber F, Pick K, Erpenbeck D, Wörheide G, Morgenstern B.

BMC Bioinformatics. 2009 Jul 16;10:219.PMID: 19607672 [PubMed - indexed for MEDLINE]Related articlesFree article

ABySS: a parallel assembler for short read sequence data.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.

Genome Res. 2009 Jun;19(6):1117-23. Epub 2009 Feb 27.PMID: 19251739 [PubMed - indexed for MEDLINE]Related articlesFree article

Crystallizing short-read assemblies around seeds.

Hossain MS, Azimi N, Skiena S.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S16.PMID: 19208115 [PubMed - indexed for MEDLINE]Related articlesFree article

Correcting short reads with high error rates for improved sequencing result.

Wong TK, Lam TW, Chan PY, Yiu SM.

Int J Bioinform Res Appl. 2009;5(2):224-37.PMID: 19324607 [PubMed - indexed for MEDLINE]Related articles

An ORFome assembly approach to metagenomics sequences analysis.

Ye Y, Tang H.

Comput Syst Bioinformatics Conf. 2008;7:3-13.PMID: 19642264 [PubMed - indexed for MEDLINE]Related articles

Profiling model T-cell metagenomes with short reads.

Warren RL, Nelson BH, Holt RA.

Bioinformatics. 2009 Feb 15;25(4):458-64. Epub 2009 Jan 9.PMID: 19136549 [PubMed - indexed for MEDLINE]Related articlesFree article

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey.

Kerstens HH, Crooijmans RP, Veenendaal A, Dibbits BW, Chin-A-Woeng TF, den Dunnen JT, Groenen MA.

BMC Genomics. 2009 Oct 16;10:479.PMID: 19835600 [PubMed - indexed for MEDLINE]Related articlesFree article