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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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Alignment identity? #165

Open jzrapp opened 2 years ago

jzrapp commented 2 years ago

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 commented 2 years ago

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