The best replacement for
bwa
is
bowtie2
.
The best alternatives to bwa are rated as following:
★★★★★
bowtie2
★★★★
axx
★★★★
tophat
★★★★
novoalign
★★★
bowtie
★★
aax
★
maq
★
hana
★
guv
bfast
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No companions for
bwa
have been suggested so far.
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bwa
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