Nature Communications · 2017 · 121 citations · 39 references
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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
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan, Ira M. Hall · Bioinformatics · 2010 · 28.9K citations · Full text
Primer3—new capabilities and interfaces
Andreas Untergasser, Ioana Cutcutache, Triinu Kõressaar et al. · Nucleic Acids Research · 2012 · 9.5K citations · Full text
<tt>BLAT</tt>—The <tt>BLAST</tt>-Like Alignment Tool
W. James Kent · Genome Research · 2002 · 8.3K citations · Full text
SOAPdenovo2: an empirically improved memory-efficient short-read <i>de novo</i> assembler
Ruibang Luo, Binghang Liu, Yinlong Xie et al. · GigaScience · 2012 · 5.5K citations · Full text