Alignment identity?

[jzrapp]

Hi @kbseah ,
is there a way for me to find out the alignment identity between individual reads and their closest database hit from the output files?

Thanks!
Josephine

[kbseah]

Hello! Unfortunately we haven't implemented an easy way to do this, and the %id histogram in the output report is based on the BBmap summary output. The SAM mapping file can be parsed to give the %id. Relevant SAM tag is the NM tag, which is the total number of mismatches + indels relative to the reference. Important to note is which definition of %id you choose to work with; there is a summary of different alternatives e.g. in the Vsearch documentation, look for the iddef parameter. Hope that this helps!
-- Brandon