1
$\begingroup$

In whole genome secondary analysis does BWA-MEM use a double stranded fasta reference or are reads aligned to only one, single stranded fasta reference?

$\endgroup$
1
$\begingroup$

BWA-mem (like most aligners), takes a normal single-stranded fasta file (I've never seen one with both strands listed) and aligns to both strand.

$\endgroup$
  • $\begingroup$ This means that BWA-MEM takes into consideration the complementary strand of each single stranded read prior to alignment? $\endgroup$ – AminomiX Jan 26 '16 at 15:24
  • $\begingroup$ Yes, all normal aligners do this. $\endgroup$ – Devon Ryan Jan 26 '16 at 19:02

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.