BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS

The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

(2014) Caterina Manzari et al.   BIOLOGICAL INVASIONS

An Illumina metabarcoding pipeline for fungi

(2014) Miklós Bálint et al.   Ecology and Evolution

Further Steps in TANGO: improved taxonomic assignment in metagenomics

(2013) D. Alonso-Alemany et al.   BIOINFORMATICS

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

A comparative evaluation of sequence classification programs

(2012) Adam L Bazinet et al.   BMC BIOINFORMATICS

Reference databases for taxonomic assignment in metagenomics

(2012) M. Santamaria et al.   BRIEFINGS IN BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

METAGENassist: a comprehensive web server for comparative metagenomics

(2012) D. Arndt et al.   NUCLEIC ACIDS RESEARCH

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Flexible taxonomic assignment of ambiguous sequencing reads

(2011) José C Clemente et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim

(2010) S. Balzer et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

Like Will to Like: Abundances of Closely Related Species Can Predict Susceptibility to Intestinal Colonization by Pathogenic and Commensal Bacteria

(2010) Bärbel Stecher et al.   PLoS Pathogens

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

(2008) Anders F. Andersson et al.   PLoS One