is -a bwtsw flag compulsory for indexing human genome with BWA?

Question

[marongiu.luigi]

hello,

I am indexing the human genome with BWA and I was wondering whether the flag -a bwtsw is compulsory or I can just use bwa index hgnn.fa and still get proper indices.

Thank you

Answer 1

[ATpoint]

Running the default setting without specifying -a is fine, as BWA will choose the proper algorithm based on the length of the genome automatically.