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Items: 1 to 20 of 96

1.

Assessing the consequences of denoising marker-based metagenomic data.

Gaspar JM, Thomas WK.

PLoS One. 2013;8(3):e60458. doi: 10.1371/journal.pone.0060458. Epub 2013 Mar 25.

2.

FlowClus: efficiently filtering and denoising pyrosequenced amplicons.

Gaspar JM, Thomas WK.

BMC Bioinformatics. 2015 Mar 27;16:105. doi: 10.1186/s12859-015-0532-1.

3.

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.

4.

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data.

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

Gigascience. 2017 Feb 1;6(2):1-10. doi: 10.1093/gigascience/giw017.

5.

IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data.

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

BMC Bioinformatics. 2016 Apr 29;17(1):192. doi: 10.1186/s12859-016-1061-2.

6.

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.

Schloss PD, Gevers D, Westcott SL.

PLoS One. 2011;6(12):e27310. doi: 10.1371/journal.pone.0027310. Epub 2011 Dec 14.

7.

Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads.

Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD.

Appl Environ Microbiol. 2011 Jun;77(11):3846-52. doi: 10.1128/AEM.02772-10. Epub 2011 Apr 1. Erratum in: Appl Environ Microbiol. 2011 Aug;77(15):5569.

8.

Removing noise from pyrosequenced amplicons.

Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ.

BMC Bioinformatics. 2011 Jan 28;12:38. doi: 10.1186/1471-2105-12-38.

9.

Parallel-META: efficient metagenomic data analysis based on high-performance computation.

Su X, Xu J, Ning K.

BMC Syst Biol. 2012;6 Suppl 1:S16. doi: 10.1186/1752-0509-6-S1-S16. Epub 2012 Jul 16.

10.

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.

11.

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.

12.

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

Albanese D, Fontana P, De Filippo C, Cavalieri D, Donati C.

Sci Rep. 2015 May 19;5:9743. doi: 10.1038/srep09743.

13.

Phoenix 2: a locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface.

Soh J, Dong X, Caffrey SM, Voordouw G, Sensen CW.

J Biotechnol. 2013 Sep 20;167(4):393-403. doi: 10.1016/j.jbiotec.2013.07.004. Epub 2013 Jul 16.

14.

Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data.

Koskinen K, Auvinen P, Björkroth KJ, Hultman J.

J Comput Biol. 2015 Aug;22(8):743-51. doi: 10.1089/cmb.2014.0268. Epub 2014 Dec 19.

PMID:
25525895
15.

MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool.

Zou B, Li J, Zhou Q, Quan ZX.

PLoS One. 2017 Mar 28;12(3):e0174609. doi: 10.1371/journal.pone.0174609. eCollection 2017.

16.

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.

Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J.

BMC Bioinformatics. 2009 Dec 18;10:430. doi: 10.1186/1471-2105-10-430.

17.

Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets.

Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH.

Res Microbiol. 2012 Jul;163(6-7):407-12. doi: 10.1016/j.resmic.2012.07.001. Epub 2012 Jul 21.

PMID:
22824070
18.

LotuS: an efficient and user-friendly OTU processing pipeline.

Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J.

Microbiome. 2014 Sep 30;2(1):30. doi: 10.1186/2049-2618-2-30.

19.

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.

20.

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.

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