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Old 02-06-2012, 02:52 AM   #1
Location: Sweden

Join Date: Jan 2011
Posts: 12
Default What are the default settings in bwa?


If I understand correctly, the default setting of bwa aln - according to the homepage - is no seeding and max 4% mismatches over the whole read length. However, when I run bwa (bwa 0.5.9-r16) it reports that the default is 32 bp seed. What are the default settings for this version?

Thank you in advance for resolving this confusing issue...
genomicist is offline   Reply With Quote

bwa, bwa aln, bwa default settings, seed

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