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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?

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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.

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  • $\begingroup$ This means that BWA-MEM takes into consideration the complementary strand of each single stranded read prior to alignment? $\endgroup$
    – AminomiX
    Jan 26, 2016 at 15:24
  • $\begingroup$ Yes, all normal aligners do this. $\endgroup$
    – Devon Ryan
    Jan 26, 2016 at 19:02

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