Hello,
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...
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...