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cimendes avatar cimendes commented on July 19, 2024

Hello!

First of all apologies for the late reply. Regarding your question about DEN-IM's update, unfortunately, it's not on our current plans to do so. DEN-IM, although still methodologically sound, is now quite outdated, as it is still in Nextflow DLS1 and the database hasn't been updated in quite a while. I checked BV-BRC and I could not find any information regarding sero and genotype in the sequences deposited, but I'll admit that I haven't looked with much attention.

Equally, the option to skip trimming won't be implemented at the time being. Maybe adjusting the trimming parameters might help with the problem you're facing.

Regarding your question about coverage from the integrity_coverage_in_1_1 and check_coverage_1_6 processes, the first is performed on the raw read set, whereas the second is done after mapping and trimming.

from den-im.

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