IVA: accuratede novoassembly of RNA virus genomes

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Disk-based k-mer counting on a PC

(2013) Sebastian Deorowicz et al.   BMC BIOINFORMATICS

PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data

(2013) J. Graham Ruby et al.   G3-Genes Genomes Genetics

De novo assembly of highly diverse viral populations

(2012) Xiao Yang et al.   BMC GENOMICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

RATT: Rapid Annotation Transfer Tool

(2011) Thomas D. Otto et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS