Fast and sensitive taxonomic classification for metagenomics with Kaiju

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs

(2015) Peter Menzel et al.   MICROBIAL ECOLOGY

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Scalable metagenomic taxonomy classification using a reference genome database

(2013) Sasha K. Ames et al.   BIOINFORMATICS

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

Long read alignment based on maximal exact match seeds

(2012) Yongchao Liu et al.   BIOINFORMATICS

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

The oral microbiome in health and disease

(2012) William G. Wade   PHARMACOLOGICAL RESEARCH

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

(2011) Y. Zhao et al.   BIOINFORMATICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts

(2008) Minghui Jiang et al.   BMC BIOINFORMATICS