search

tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
GNU General Public License v2.0
201 stars 47 forks source link

Does not detect allele if it´s present in reverse orientation? False #97

Closed mdiricks closed 4 years ago

mdiricks commented 4 years ago

I have samples for which I don´t get a valid allele call although I know the allele is present in one of the contigs (I give a multifasta file as input), but in reverse complement. Does this script not take into account reverse complement sequences?

mdiricks commented 4 years ago

It does detect sequences in reverse orientation. I got results for my sample only if I indicate the scheme in the command

tseemann commented 4 years ago

You can run with --verbose to see more info.

I am guessing you aren't reaching --minscore to report the matches in auto mode?

mdiricks commented 4 years ago

Thanks for your answer! verbose is an unknown function? Must be indeed that I don`t reach --minscore somehow. Haemophilus is genetically quite diverse, so could be due to that

tseemann commented 4 years ago

sorry wrong name:

--debug Verbose debug output to stderr (default OFF)