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Items: 1 to 20 of 173

1.

Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.

Wu YW, Rho M, Doak TG, Ye Y.

Bioinformatics. 2012 Sep 15;28(18):i363-i369. doi: 10.1093/bioinformatics/bts388.

2.

Evaluation of short read metagenomic assembly.

Charuvaka A, Rangwala H.

BMC Genomics. 2011;12 Suppl 2:S8. doi: 10.1186/1471-2164-12-S2-S8. Epub 2011 Jul 27.

3.

Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut.

Vázquez-Castellanos JF, García-López R, Pérez-Brocal V, Pignatelli M, Moya A.

BMC Genomics. 2014 Jan 18;15:37. doi: 10.1186/1471-2164-15-37.

4.

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.

Namiki T, Hachiya T, Tanaka H, Sakakibara Y.

Nucleic Acids Res. 2012 Nov 1;40(20):e155. doi: 10.1093/nar/gks678. Epub 2012 Jul 19.

5.

Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations.

García-López R, Vázquez-Castellanos JF, Moya A.

Front Bioeng Biotechnol. 2015 Sep 17;3:141. doi: 10.3389/fbioe.2015.00141. eCollection 2015.

6.

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis.

Ye Y, Tang H.

Bioinformatics. 2016 Apr 1;32(7):1001-8. doi: 10.1093/bioinformatics/btv510. Epub 2015 Aug 29.

7.

Meta-IDBA: a de Novo assembler for metagenomic data.

Peng Y, Leung HC, Yiu SM, Chin FY.

Bioinformatics. 2011 Jul 1;27(13):i94-101. doi: 10.1093/bioinformatics/btr216.

8.

Bambus 2: scaffolding metagenomes.

Koren S, Treangen TJ, Pop M.

Bioinformatics. 2011 Nov 1;27(21):2964-71. doi: 10.1093/bioinformatics/btr520. Epub 2011 Sep 16.

9.

SPA: a short peptide assembler for metagenomic data.

Yang Y, Yooseph S.

Nucleic Acids Res. 2013 Apr;41(8):e91. doi: 10.1093/nar/gkt118. Epub 2013 Feb 23.

10.

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.

Peng Y, Leung HC, Yiu SM, Chin FY.

Bioinformatics. 2012 Jun 1;28(11):1420-8. doi: 10.1093/bioinformatics/bts174. Epub 2012 Apr 11.

11.

Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation.

Celaj A, Markle J, Danska J, Parkinson J.

Microbiome. 2014 Oct 28;2:39. doi: 10.1186/2049-2618-2-39. eCollection 2014.

12.

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.

13.

Reference-independent comparative metagenomics using cross-assembly: crAss.

Dutilh BE, Schmieder R, Nulton J, Felts B, Salamon P, Edwards RA, Mokili JL.

Bioinformatics. 2012 Dec 15;28(24):3225-31. doi: 10.1093/bioinformatics/bts613. Epub 2012 Oct 16.

14.

MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.

Reddy RM, Mohammed MH, Mande SS.

Genomics. 2014 Feb-Mar;103(2-3):161-8. doi: 10.1016/j.ygeno.2014.02.007. Epub 2014 Mar 5.

15.

Omega: an overlap-graph de novo assembler for metagenomics.

Haider B, Ahn TH, Bushnell B, Chai J, Copeland A, Pan C.

Bioinformatics. 2014 Oct;30(19):2717-22. doi: 10.1093/bioinformatics/btu395. Epub 2014 Jun 19.

16.

MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks.

Gori F, Folino G, Jetten MS, Marchiori E.

Bioinformatics. 2011 Jan 15;27(2):196-203. doi: 10.1093/bioinformatics/btq649. Epub 2010 Dec 1.

17.

MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning.

Wang Y, Leung H, Yiu S, Chin F.

BMC Genomics. 2014;15 Suppl 1:S12. doi: 10.1186/1471-2164-15-S1-S12. Epub 2014 Jan 24.

18.

A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.

Zhang Y, Sun Y, Cole JR.

PLoS Comput Biol. 2014 Aug 14;10(8):e1003737. doi: 10.1371/journal.pcbi.1003737. eCollection 2014 Aug.

19.

The effect of sequencing errors on metagenomic gene prediction.

Hoff KJ.

BMC Genomics. 2009 Nov 12;10:520. doi: 10.1186/1471-2164-10-520.

20.

FragGeneScan: predicting genes in short and error-prone reads.

Rho M, Tang H, Ye Y.

Nucleic Acids Res. 2010 Nov;38(20):e191. doi: 10.1093/nar/gkq747. Epub 2010 Aug 30.

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