Determine if contig terminates at 3' end of genome

ababaian / serratus

Ultra-deep search for novel viruses

http://serratus.io

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Determine if contig terminates at 3' end of genome #175

Closed rcedgar closed 4 years ago

rcedgar commented 4 years ago

We need to know if an assembly ends at the 3' end of the genome. The genome is expected to end with poly-A, but apparently this is trimmed by the assembler as a QC step.

Open problem: how to determine if a contig ends at the 3' end of the genome.

taltman commented 4 years ago

I think this can be handled by VADR, I'll just need to figure out the correct output file to mine for this info.

rcedgar commented 4 years ago

Solved as in #176, use RFAM HMMs or blastn to UTRs.