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tseemann / legsta

🍗⭐ In silico Legionella pneumophila Sequence Based Typing
GNU General Public License v3.0
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Hi Torsen #11

Closed EricFournier3 closed 4 years ago

EricFournier3 commented 4 years ago

Hi Torsen, i am wondering if the script works fine with concatenation of the 7 sequences in one fasta file instead of a whole genome sequence. We have only data from first generation sequencing. Actually, i tried it and it doesn't works.

Thanks Eric

tseemann commented 4 years ago

@EricFournier3 it probably will not work because it relies in in silico PCR so if you don't have the primers in the template you sequenced it won't be able to find the amplicons? The primers are essential to distinguising the mompS paralog.

However, you could make an mlst database from the SBT files and use mlst because that uses the sequence alone.