Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Using cascading Bloom filters to improve the memory usage for de Brujin graphs

(2014) Kamil Salikhov et al.   Algorithms for Molecular Biology

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

GATB: Genome Assembly & Analysis Tool Box

(2014) Erwan Drezen et al.   BIOINFORMATICS

Reference-free detection of isolated SNPs

(2014) Raluca Uricaru et al.   NUCLEIC ACIDS RESEARCH

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

(2013) Rayan Chikhi et al.   Algorithms for Molecular Biology

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment

(2013) Daniel J. Kvitek et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer

(2012) Pierre Peterlongo et al.   BMC BIOINFORMATICS

Structure, fluctuation and magnitude of a natural grassland soil metagenome

(2012) Tom O Delmont et al.   ISME Journal

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Accessing the Soil Metagenome for Studies of Microbial Diversity

(2010) Tom O. Delmont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

(2009) Nicolas Philippe 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