RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets

Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data

(2014) Allyson L Byrd et al.   BMC BIOINFORMATICS

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

MetaGeniE: Characterizing Human Clinical Samples Using Deep Metagenomic Sequencing

(2014) Arun Rawat et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

(2013) Sarah Hunter et al.   NUCLEIC ACIDS RESEARCH

Avian bornaviruses are widely distributed in canary birds (Serinus canaria f. domestica)

(2013) Dennis Rubbenstroth et al.   VETERINARY MICROBIOLOGY

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

(2012) Lukas Habegger et al.   BIOINFORMATICS

Rapid identification of non-human sequences in high-throughput sequencing datasets

(2012) Aparna Bhaduri et al.   BIOINFORMATICS

READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation

(2012) Raeece Naeem et al.   BIOINFORMATICS

Functional assignment of metagenomic data: challenges and applications

(2012) T. Prakash et al.   BRIEFINGS IN BIOINFORMATICS

Bioinformatic approaches for functional annotation and pathway inference in metagenomics data

(2012) C. De Filippo et al.   BRIEFINGS IN BIOINFORMATICS

Ultrafast clustering algorithms for metagenomic sequence analysis

(2012) W. Li et al.   BRIEFINGS IN BIOINFORMATICS

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing

(2012) Jana Sachsenröder et al.   PLoS One

DNase SISPA-Next Generation Sequencing Confirms Schmallenberg Virus in Belgian Field Samples and Identifies Genetic Variation in Europe

(2012) Toon Rosseel et al.   PLoS One

MetaABC—an integrated metagenomics platform for data adjustment, binning and clustering

(2011) Chien-Hao Su et al.   BIOINFORMATICS

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

(2011) Beifang Niu et al.   BIOINFORMATICS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases

(2008) Gustavo Palacios et al.   NEW ENGLAND JOURNAL OF MEDICINE