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Results: 1 to 20 of 93

1.

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M.

Genome Biol. 2013 Jan 15;14(1):R2. doi: 10.1186/gb-2013-14-1-r2.

PMID:
23320958
[PubMed - in process]
2.

The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data.

Lammers Y, Peelen T, Vos RA, Gravendeel B.

BMC Bioinformatics. 2014 Feb 6;15:44. doi: 10.1186/1471-2105-15-44.

PMID:
24502833
[PubMed - indexed for MEDLINE]
3.

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach.

Hahn C, Bachmann L, Chevreux B.

Nucleic Acids Res. 2013 Jul;41(13):e129. doi: 10.1093/nar/gkt371. Epub 2013 May 9.

PMID:
23661685
[PubMed - indexed for MEDLINE]
4.

A filtering method to generate high quality short reads using illumina paired-end technology.

Eren AM, Vineis JH, Morrison HG, Sogin ML.

PLoS One. 2013 Jun 17;8(6):e66643. doi: 10.1371/journal.pone.0066643. Print 2013. Erratum in: PLoS One. 2013;8(6). doi:10.1371/annotation/afa5c40d-c604-46ae-84c4-82cb92193a5e.

PMID:
23799126
[PubMed - indexed for MEDLINE]
5.

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]
6.

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.

PMID:
25122209
[PubMed - in process]
7.

Evaluating the fidelity of de novo short read metagenomic assembly using simulated data.

Pignatelli M, Moya A.

PLoS One. 2011;6(5):e19984. doi: 10.1371/journal.pone.0019984. Epub 2011 May 23.

PMID:
21625384
[PubMed - indexed for MEDLINE]
8.

MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads.

Tyakht AV, Popenko AS, Belenikin MS, Altukhov IA, Pavlenko AV, Kostryukova ES, Selezneva OV, Larin AK, Karpova IY, Alexeev DG.

Source Code Biol Med. 2012 Dec 7;7(1):13. doi: 10.1186/1751-0473-7-13.

PMID:
23216677
[PubMed]
9.

Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.

Sharma VK, Kumar N, Prakash T, Taylor TD.

PLoS One. 2012;7(4):e34030. doi: 10.1371/journal.pone.0034030. Epub 2012 Apr 4.

PMID:
22496776
[PubMed - indexed for MEDLINE]
10.

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.

PMID:
23049702
[PubMed - indexed for MEDLINE]
11.

MOCAT: a metagenomics assembly and gene prediction toolkit.

Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P.

PLoS One. 2012;7(10):e47656. doi: 10.1371/journal.pone.0047656. Epub 2012 Oct 17.

PMID:
23082188
[PubMed - indexed for MEDLINE]
12.

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.

PMID:
21989307
[PubMed - indexed for MEDLINE]
13.

Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization.

Su X, Pan W, Song B, Xu J, Ning K.

PLoS One. 2014 Mar 3;9(3):e89323. doi: 10.1371/journal.pone.0089323. eCollection 2014.

PMID:
24595159
[PubMed - in process]
14.

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots.

Kumar S, Jones M, Koutsovoulos G, Clarke M, Blaxter M.

Front Genet. 2013 Nov 29;4:237. doi: 10.3389/fgene.2013.00237. eCollection 2013.

PMID:
24348509
[PubMed]
15.

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.

PMID:
21127032
[PubMed - indexed for MEDLINE]
16.

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm.

Wu YW, Tang YH, Tringe SG, Simmons BA, Singer SW.

Microbiome. 2014 Aug 1;2:26. doi: 10.1186/2049-2618-2-26. eCollection 2014.

PMID:
25136443
[PubMed]
17.

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.

PMID:
21685107
[PubMed - indexed for MEDLINE]
18.

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.

PMID:
24438450
[PubMed - indexed for MEDLINE]
19.

Functional assignment of metagenomic data: challenges and applications.

Prakash T, Taylor TD.

Brief Bioinform. 2012 Nov;13(6):711-27. doi: 10.1093/bib/bbs033. Epub 2012 Jul 6. Review.

PMID:
22772835
[PubMed - indexed for MEDLINE]
20.

Conservation of gene cassettes among diverse viruses of the human gut.

Minot S, Wu GD, Lewis JD, Bushman FD.

PLoS One. 2012;7(8):e42342. doi: 10.1371/journal.pone.0042342. Epub 2012 Aug 10.

PMID:
22900013
[PubMed - indexed for MEDLINE]

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