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Analytical tools and databases for metagenomics in the next-generation sequencing era

veröffentlicht in: Genomics & Informatics

Erscheinungsdatum: 2013-09-30

Hauptthema: Datenbank, Metagenomik

Zitiert Artikel 109

Datum

Titel

Autor

2012-12-22

Ray Meta: scalable de novo metagenome assembly and profiling

Frédéric Raymond, Jacques Corbeil
2012-12-10

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

Byron J. Adams, Noah Fierer, Uffe N. Nielsen, Diana H. Wall, J Gregory Caporaso, Jack A Gilbert
2012-11-29

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Jianyi Lin, Pablo Minguez, Peer Bork, Christian von Mering, Lars Juhl Jensen, Milan Simonovic, Andrea Franceschini, Damian Szklarczyk
2012-11-28

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Elmar Pruesse, Pelin Yilmaz, Frank Oliver Glöckner, Christian Quast
2012-10-31

Denoising PCR-amplified metagenome data

Susan P. Holmes
2012-10-11

CD-HIT: accelerated for clustering the next-generation sequencing data

Weizhong Li
2012-10

Single cell genomics: an individual look at microbes

Ramunas Stepanauskas
2012-09-27

Secondary structure improves OTU assignments of 16S rRNA gene sequences

Patrick D. Schloss
2012-09-09

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

Frank Oliver Glöckner
2012-08-02

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

Martin Hartmann, Richard Christen, Steven James Hallam, William W. Mohn
2012-07-19

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
2012-07-06

Functional assignment of metagenomic data: challenges and applications

Todd D Taylor
2012-08

Metagenomic microbial community profiling using unique clade-specific marker genes

Curtis Huttenhower, Vagheesh Narasimhan, Nicola Segata, Olivier Jousson, Levi Waldron, Annalisa Ballarini
2012-08

Rapid identification of high-confidence taxonomic assignments for metagenomic data
2012-03-05

Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms
2012-02-16

Joint analysis of multiple metagenomic samples
2012-02-12

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.

Alexandra J. Scott, Martin Wu
2012-01-12

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

Rob Knight, Neelendu Dey, Steven Elliot Brenner
2012-01

The Pfam protein families database

Alex Bateman, Sean Eddy, Robert D. Finn, Jody Clements, Jaina Mistry, Goran Ceric, Sofia Forslund, Erik Sonnhammer, Ruth Y. Eberhardt, Andreas Heger, Marco Punta, Penny C. Coggill, John G. Tate, Chris Boursnell, Ningze Pang, Liisa Holm
2012-01

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Kate Dreher, Peter D. Karp, Markus Krummenacker, Lukas A Mueller
2012-01

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering

Mihai Pop, Steven Salzberg, Arthur L. Delcher
2012-01

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

Peer Bork, Ivica Letunic, Damian Szklarczyk, Christian von Mering, Lars Juhl Jensen, Tobias Doerks, Jean Muller, Thomas Rattei, Sean T Powell, Kalliopi Trachana
2012-01

IMG/M: the integrated metagenome data management and comparative analysis system

Natalia Ivanova, Nikos C. Kyrpides, Amrita Pati, Marcel Huntemann, Iain J. Anderson, Konstantinos Mavromatis, Krishna Palaniappan, Victor Markowitz, Ernest Szeto, Ioanna Pagani, Yuri Grechkin, Biju Jacob, Konstantinos Liolios
2012-04-11

A de novo metagenomic assembly program for shotgun DNA reads

Binbin Lai
2012-05-03

SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes

Elmar Pruesse, Frank Oliver Glöckner
2012-04-27

Fast, accurate error-correction of amplicon pyrosequences using Acacia.

Philip Hugenholtz, Gene W. Tyson
2012-04-27

TBC: a clustering algorithm based on prokaryotic taxonomy.
2012-01-01

SEPP: SATé-enabled phylogenetic placement.
2011-12-14

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

Patrick D. Schloss, Dirk Gevers
2011-11-25

Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
2011-11-18

DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences

Daniel R Noguera
2011-10

Accelerated Profile HMM Searches

Sean Eddy

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