Genome biology · 2020 · 86 citations · 42 references
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The Sequence Alignment/Map format and SAMtools
Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 64.7K citations · Full text
Fast gapped-read alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 58.3K citations · Full text
Long-read Sequencing, Sequence Assembly, Natural Sciences +7
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna, Matthew G. Hanna, Eric Banks et al. · Genome Research · 2010 · 28.9K citations · Full text
The variant call format and VCFtools
Petr Danecek, Adam Auton, Gonçalo R. Abecasis et al. · Bioinformatics · 2011 · 16.8K citations · Full text
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff
Pablo Cingolani, Adrian E. Platts, Le Lily Wang et al. · Fly · 2012 · 12.1K citations · Full text