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Items: 1 to 20 of 112

1.

Filtering duplicate reads from 454 pyrosequencing data.

Balzer S, Malde K, Grohme MA, Jonassen I.

Bioinformatics. 2013 Apr 1;29(7):830-6. doi: 10.1093/bioinformatics/btt047. Epub 2013 Feb 1.

2.

Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim.

Balzer S, Malde K, Lanzén A, Sharma A, Jonassen I.

Bioinformatics. 2010 Sep 15;26(18):i420-5. doi: 10.1093/bioinformatics/btq365. Erratum in: Bioinformatics. 2011 Aug 1;27(15):2171.

3.

Artificial and natural duplicates in pyrosequencing reads of metagenomic data.

Niu B, Fu L, Sun S, Li W.

BMC Bioinformatics. 2010 Apr 13;11:187. doi: 10.1186/1471-2105-11-187.

4.

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.

5.

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.

6.

Bayexer: an accurate and fast Bayesian demultiplexer for Illumina sequences.

Yi H, Li Z, Li T, Zhao J.

Bioinformatics. 2015 Dec 15;31(24):4000-2. doi: 10.1093/bioinformatics/btv501. Epub 2015 Aug 26.

PMID:
26315903
7.

RBR: library-less repeat detection for ESTs.

Malde K, Schneeberger K, Coward E, Jonassen I.

Bioinformatics. 2006 Sep 15;22(18):2232-6. Epub 2006 Jul 12.

PMID:
16837527
8.

Efficient alignment of pyrosequencing reads for re-sequencing applications.

Fernandes F, da Fonseca PG, Russo LM, Oliveira AL, Freitas AT.

BMC Bioinformatics. 2011 May 16;12:163. doi: 10.1186/1471-2105-12-163.

9.

A de novo metagenomic assembly program for shotgun DNA reads.

Lai B, Ding R, Li Y, Duan L, Zhu H.

Bioinformatics. 2012 Jun 1;28(11):1455-62. doi: 10.1093/bioinformatics/bts162. Epub 2012 Apr 11.

PMID:
22495746
10.

Bayesian mixture analysis for metagenomic community profiling.

Morfopoulou S, Plagnol V.

Bioinformatics. 2015 Sep 15;31(18):2930-8. doi: 10.1093/bioinformatics/btv317. Epub 2015 May 21.

11.

Systematic exploration of error sources in pyrosequencing flowgram data.

Balzer S, Malde K, Jonassen I.

Bioinformatics. 2011 Jul 1;27(13):i304-9. doi: 10.1093/bioinformatics/btr251.

12.

Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Li H, Ruan J, Durbin R.

Genome Res. 2008 Nov;18(11):1851-8. doi: 10.1101/gr.078212.108. Epub 2008 Aug 19.

13.

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.

PMID:
24919879
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.

15.

BLESS: bloom filter-based error correction solution for high-throughput sequencing reads.

Heo Y, Wu XL, Chen D, Ma J, Hwu WM.

Bioinformatics. 2014 May 15;30(10):1354-62. doi: 10.1093/bioinformatics/btu030. Epub 2014 Jan 21.

PMID:
24451628
16.

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads.

Mysara M, Leys N, Raes J, Monsieurs P.

BMC Bioinformatics. 2015 Mar 15;16:88. doi: 10.1186/s12859-015-0520-5.

17.

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.

Gritsenko AA, Nijkamp JF, Reinders MJ, de Ridder D.

Bioinformatics. 2012 Jun 1;28(11):1429-37. doi: 10.1093/bioinformatics/bts175. Epub 2012 Apr 6.

PMID:
22492642
18.

Aggressive assembly of pyrosequencing reads with mates.

Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G.

Bioinformatics. 2008 Dec 15;24(24):2818-24. doi: 10.1093/bioinformatics/btn548. Epub 2008 Oct 24.

19.

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.

20.

Bias from removing read duplication in ultra-deep sequencing experiments.

Zhou W, Chen T, Zhao H, Eterovic AK, Meric-Bernstam F, Mills GB, Chen K.

Bioinformatics. 2014 Apr 15;30(8):1073-1080. Epub 2014 Jan 2.

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