Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin · Bioinformatics · 2009 · 62.8K citations · Full text

Life Sciences, Bioinformatics, Biology +12

Fast gapped-read alignment with Bowtie 2

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

Life Sciences, Bioinformatics, Molecular Biology +11

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

The GEM mapper: fast, accurate and versatile alignment by filtration

Santiago Marco‐Sola, Michael Sammeth, Roderic Guigó et al. · Nature Methods · 2012 · 594 citations · Full text

Computing, Geoinformatics, Data Structures +2

Striped Smith–Waterman speeds database searches six times over other SIMD implementations

Michael S. Farrar · Bioinformatics · 2006 · 450 citations · Full text

Computing, Computer Engineering, Computer Science +17