Does salmon use phred scores while pseudoaligning (and/or validating mapping)?
Entering edit mode
2.6 years ago
Anthony • 0

Dear Biostar Community,

I would like to know if salmon uses phred scores while pseudoaligning (and/or validating mapping)?

In the negative, what is the reason behind this the choice?

Thanks in advance,


Salmon phred • 767 views
Entering edit mode
2.6 years ago
Rob 5.0k

Hi Anthony,

No; salmon does not use the PHRED score, either while mapping or aligning. The main reason for not using it during alignment or mapping is that it just tends not to be very useful for this purpose. If a nucleotide inside a reasonably long exact match is bad quality (and therefore likely wrong), it’s almost certainly wrong in all of the mappings where it appears. In terms of finding the best locus (or loci) for the read, the quality score just turns out not to be very useful, while using it incurs extra processing cycles. Clearly, there _are_ cases where the quality scores are useful (e.g. in downstream variant detection, etc.) — however, we found them not to be helpful for our purposes and so we don’t use them.

Best, Rob


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