NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.

PubWeight™: 0.79‹?›

🔗 View Article (PMC 4489229)

Published in Nucleic Acids Res on April 15, 2015

Authors

Ali May1, Sanne Abeln2, Mark J Buijs3, Jaap Heringa2, Wim Crielaard3, Bernd W Brandt4

Author Affiliations

1: Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands.
2: Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands AIMMS Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, Amsterdam, The Netherlands.
3: Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands.
4: Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands b.brandt@acta.nl.

Articles cited by this

QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol (2009) 77.55

EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet (2000) 69.26

A core gut microbiome in obese and lean twins. Nature (2008) 52.30

Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 51.97

Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A (2006) 42.38

Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A (1985) 37.69

Structure, function and diversity of the healthy human microbiome. Nature (2012) 30.40

UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (2011) 29.22

The NIH Human Microbiome Project. Genome Res (2009) 24.61

Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol (2007) 23.64

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A (2010) 19.48

Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol (1991) 18.78

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21

Removing noise from pyrosequenced amplicons. BMC Bioinformatics (2011) 13.45

Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol (2010) 13.19

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One (2011) 12.26

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A (2012) 10.22

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics (2012) 9.97

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods (2010) 9.18

Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol (2012) 8.99

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol (2013) 8.53

Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev (2004) 7.95

Human colonic biota studied by ribosomal DNA sequence analysis. Appl Environ Microbiol (1996) 6.98

Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl Environ Microbiol (1993) 5.60

Bacterial phylogeny based on comparative sequence analysis. Electrophoresis (1998) 5.59

Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature (2001) 5.25

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol (2010) 4.97

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics (2011) 4.39

Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol (2007) 4.32

Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol (2006) 2.76

Updating benchtop sequencing performance comparison. Nat Biotechnol (2013) 2.66

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Res (2011) 2.27

A survey of error-correction methods for next-generation sequencing. Brief Bioinform (2012) 2.02

Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains. J Mol Evol (1999) 1.91

SNPServer: a real-time SNP discovery tool. Nucleic Acids Res (2005) 1.42

A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE. PLoS Comput Biol (2012) 1.18

Comparing clustering and pre-processing in taxonomy analysis. Bioinformatics (2012) 1.06

QualitySNPng: a user-friendly SNP detection and visualization tool. Nucleic Acids Res (2013) 0.98

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. Bioinformatics (2014) 0.97

Articles by these authors

metaModules identifies key functional subnetworks in microbiome-related disease. Bioinformatics (2015) 0.77