Kraken: ultrafast metagenomic sequence classification using exact alignments

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

GAGE-B: an evaluation of genome assemblers for bacterial organisms

(2013) Tanja Magoc et al.   BIOINFORMATICS

Scalable metagenomic taxonomy classification using a reference genome database

(2013) Sasha K. Ames et al.   BIOINFORMATICS

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

Salivary proteins promote proteolytic activity in Streptococcus mitis biovar 2 and Streptococcus mutans

(2012) C. Kindblom et al.   Molecular Oral Microbiology

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

PhymmBL expanded: confidence scores, custom databases, parallelization and more

(2011) Arthur Brady et al.   NATURE METHODS

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS