Reference-independent comparative metagenomics using cross-assembly: crAss

SEQanswers: an open access community for collaboratively decoding genomes

(2012) Jing-Woei Li et al.   BIOINFORMATICS

Grinder: a versatile amplicon and shotgun sequence simulator

(2012) Florent E. Angly et al.   NUCLEIC ACIDS RESEARCH

Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

(2012) Amaro E. Trindade-Silva et al.   PLoS One

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in Virology

Comparative studies of de novo assembly tools for next-generation sequencing technologies

(2011) Yong Lin et al.   BIOINFORMATICS

FACIL: Fast and Accurate Genetic Code Inference and Logo

(2011) Bas E. Dutilh et al.   BIOINFORMATICS

Systematic exploration of error sources in pyrosequencing flowgram data

(2011) S. Balzer et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences

(2011) Tarini Ghosh et al.   BMC BIOINFORMATICS

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph

(2011) Z. Li et al.   Briefings in Functional Genomics

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

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

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Metagenomic signatures of 86 microbial and viral metagenomes

(2009) Dana Willner et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic analysis of viruses in reclaimed water

(2009) Karyna Rosario et al.   ENVIRONMENTAL MICROBIOLOGY

Direct Metagenomic Detection of Viral Pathogens in Nasal and Fecal Specimens Using an Unbiased High-Throughput Sequencing Approach

(2009) Shota Nakamura et al.   PLoS One

High Diversity of the Viral Community from an Antarctic Lake

(2009) A. Lopez-Bueno et al.   SCIENCE

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH