Lambda: the local aligner for massive biological data

A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA

(2013) D. H. Huson et al.   BIOINFORMATICS

Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms

(2013) Felix G Eikmeyer et al.   Biotechnology for Biofuels

Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism

(2013) Sasha G Tetu et al.   ISME Journal

Fast and accurate read mapping with approximate seeds and multiple backtracking

(2013) Enrico Siragusa et al.   NUCLEIC ACIDS RESEARCH

SANS: high-throughput retrieval of protein sequences allowing 50% mismatches

(2012) J. P. Koskinen et al.   BIOINFORMATICS

RazerS 3: Faster, fully sensitive read mapping

(2012) David Weese et al.   BIOINFORMATICS

A comparative evaluation of sequence classification programs

(2012) Adam L Bazinet et al.   BMC BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

STELLAR: fast and exact local alignments

(2011) Birte Kehr et al.   BMC BIOINFORMATICS

RAPSearch: a fast protein similarity search tool for short reads

(2011) Yuzhen Ye et al.   BMC BIOINFORMATICS

Comparative fecal metagenomics unveils unique functional capacity of the swine gut

(2011) Regina Lamendella et al.   BMC MICROBIOLOGY

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

(2011) Rachel Mackelprang et al.   NATURE

Taxonomic classification of metagenomic shotgun sequences with CARMA3

(2011) Wolfgang Gerlach et al.   NUCLEIC ACIDS RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

MicroRazerS: rapid alignment of small RNA reads

(2009) A.-K. Emde et al.   BIOINFORMATICS

Automated Alphabet Reduction for Protein Datasets

(2009) Jaume Bacardit et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

RazerS--fast read mapping with sensitivity control

(2009) D. Weese et al.   GENOME RESEARCH

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH