Identification of Mutations in Laboratory-Evolved Microbes from Next-Generation Sequencing Data Using breseq

The variant call format and VCFtools

Petr Danecek, Adam Auton, Gonçalo R. Abecasis et al. · Bioinformatics · 2011 · 17.8K citations · Full text

Life Sciences, Bioinformatics, Genetics +17

A framework for variation discovery and genotyping using next-generation DNA sequencing data

Mark A. DePristo, Eric Banks, Ryan Poplin et al. · Nature Genetics · 2011 · 12.4K citations · Full text

Life Sciences, Bioinformatics, Genetics +14

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Helga Thorvaldsdóttir, James Robinson, Jill P. Mesirov · Briefings in Bioinformatics · 2012 · 9.8K citations · Full text

Computing, Bioinformatics, Visualization +15

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

Daniel R. Zerbino, Ewan Birney · Genome Research · 2008 · 9.7K citations · Full text

Life Sciences, Bioinformatics, Biology +14

Versatile and open software for comparing large genomes

Stefan Kurtz, Adam M. Phillippy, Arthur L. Delcher et al. · Genome biology · 2004 · 5.8K citations · Full text

Life Sciences, Bioinformatics, Evolutionary Biology +17