AXIOME: automated exploration of microbial diversity

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Targeted recovery of novel phylogenetic diversity from next-generation sequence data

(2012) Michael D J Lynch et al.   ISME Journal

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data

(2011) Xingpeng Jiang et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

PANGEA: pipeline for analysis of next generation amplicons

(2010) Adriana Giongo et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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