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Items: 1 to 20 of 190

1.

Genometa--a fast and accurate classifier for short metagenomic shotgun reads.

Davenport CF, Neugebauer J, Beckmann N, Friedrich B, Kameri B, Kokott S, Paetow M, Siekmann B, Wieding-Drewes M, Wienhöfer M, Wolf S, Tümmler B, Ahlers V, Sprengel F.

PLoS One. 2012;7(8):e41224. doi: 10.1371/journal.pone.0041224. Epub 2012 Aug 21.

2.

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
3.

Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.

Riesenfeld SJ, Pollard KS.

BMC Genomics. 2013 Jun 22;14:419. doi: 10.1186/1471-2164-14-419.

4.

Combining gene prediction methods to improve metagenomic gene annotation.

Yok NG, Rosen GL.

BMC Bioinformatics. 2011 Jan 13;12:20. doi: 10.1186/1471-2105-12-20.

5.

QC-Chain: fast and holistic quality control method for next-generation sequencing data.

Zhou Q, Su X, Wang A, Xu J, Ning K.

PLoS One. 2013;8(4):e60234. doi: 10.1371/journal.pone.0060234. Epub 2013 Apr 2.

6.

Compareads: comparing huge metagenomic experiments.

Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P.

BMC Bioinformatics. 2012;13 Suppl 19:S10. doi: 10.1186/1471-2105-13-S19-S10. Epub 2012 Dec 19.

7.

Accurate taxonomic assignment of short pyrosequencing reads.

Clemente JC, Jansson J, Valiente G.

Pac Symp Biocomput. 2010:3-9.

8.

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.

PMID:
22495754
9.

Phylogeny-based classification of microbial communities.

Tanaseichuk O, Borneman J, Jiang T.

Bioinformatics. 2014 Feb 15;30(4):449-56. doi: 10.1093/bioinformatics/btt700. Epub 2013 Dec 24.

PMID:
24369151
10.

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.

Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M.

BMC Genomics. 2011;12 Suppl 2:S4. doi: 10.1186/1471-2164-12-S2-S4. Epub 2011 Jul 27.

11.

Evaluating the Quantitative Capabilities of Metagenomic Analysis Software.

Kerepesi C, Grolmusz V.

Curr Microbiol. 2016 May;72(5):612-6. doi: 10.1007/s00284-016-0991-2. Epub 2016 Jan 30.

PMID:
26831696
12.
13.

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.

14.

Flexible taxonomic assignment of ambiguous sequencing reads.

Clemente JC, Jansson J, Valiente G.

BMC Bioinformatics. 2011 Jan 7;12:8. doi: 10.1186/1471-2105-12-8.

15.

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms.

Liu J, Wang H, Yang H, Zhang Y, Wang J, Zhao F, Qi J.

Nucleic Acids Res. 2013 Jan 7;41(1):e3. doi: 10.1093/nar/gks828. Epub 2012 Aug 31.

16.

A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.

Jiang H, An L, Lin SM, Feng G, Qiu Y.

PLoS One. 2012;7(10):e46450. doi: 10.1371/journal.pone.0046450. Epub 2012 Oct 1. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/c08da7e7-60fe-4f7d-a457-299bf9f24148.

17.

TWARIT: an extremely rapid and efficient approach for phylogenetic classification of metagenomic sequences.

Reddy RM, Mohammed MH, Mande SS.

Gene. 2012 Sep 1;505(2):259-65. doi: 10.1016/j.gene.2012.06.014. Epub 2012 Jun 15.

PMID:
22710135
18.

Peptide markers of aminoacyl tRNA synthetases facilitate taxa counting in metagenomic data.

Persi E, Weingart U, Freilich S, Horn D.

BMC Genomics. 2012 Feb 10;13:65. doi: 10.1186/1471-2164-13-65.

19.

CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads.

Borozan I, Ferretti V.

Bioinformatics. 2016 Feb 1;32(3):453-5. doi: 10.1093/bioinformatics/btv587. Epub 2015 Oct 9.

20.

MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression.

Kim M, Zhang X, Ligo JG, Farnoud F, Veeravalli VV, Milenkovic O.

BMC Bioinformatics. 2016 Feb 19;17:94. doi: 10.1186/s12859-016-0932-x.

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