MetAMOS: a metagenomic assembly and analysis pipeline for AMOS

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

(2011) Ozkan U Nalbantoglu et al.   BMC BIOINFORMATICS

Genovo: De Novo Assembly for Metagenomes

(2011) Jonathan Laserson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS