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Published 20 hours ago • verified publisher icon dib-lab

explore protein-based decontamination

Open ctb opened this issue 4 years ago • 2 comments

this is not a "soon" issue, but there appears to be substantial opportunity for using amino acid k-mers to find contamination...

e.g. https://github.com/bluegenes/2020-gtdb-smash/issues/1

ctb avatar Jun 24 '20 13:06 ctb

trying this out now @bluegenes request, over in #120

ctb avatar Jul 08 '20 13:07 ctb

if we're serious about this, should probably plan on running prokka to extract proteins. or maybe six-frame translation of DNA is better, b/c could catch fragmented genes w/o reducing specificity?

ctb avatar Jul 09 '20 12:07 ctb