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

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

assembly genome sequence

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written 8.4 years ago by marongiu.luigi

1 answer

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

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written 8.4 years ago by ATpoint

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