Shotgun metagenomic sequencing reveals the full taxonomic, trophic, and functional diversity of a coral reef benthic cyanobacterial mat from Bonaire, Caribbean Netherlands

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations

Life Sciences, Bioinformatics, Molecular Biology +11

Cutadapt removes adapter sequences from high-throughput sequencing reads

Marcel Martin · EMBnet journal · 2011 · 35.8K citations · Full text

Life Sciences, Bioinformatics, Molecular Biology +8

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Weizhong Li, Adam Godzik · Bioinformatics · 2006 · 12.1K citations · Full text

Life Sciences, Bioinformatics, Computational Biology +11

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi et al. · Bioinformatics · 2013 · 11.5K citations · Full text

Life Sciences, Bioinformatics, Biology +14

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct <i>de Bruijn</i> graph

Dinghua Li, Chi-Man Liu, Ruibang Luo et al. · Bioinformatics · 2015 · 10K citations · Full text

Life Sciences, Bioinformatics, Genome Assembly +11