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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
GNU General Public License v2.0
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Extracting allelle sequence information from sample whole genome #73

Closed Nits11 closed 5 years ago

Nits11 commented 5 years ago

Hi Torsten,

Does this program can also generate an output file of MLST allele sequences for the sample sequences? I guess during the process of sequences alignment for allele type search, program finds an alignment hit in the sample sequence with one of target gene scheme sequences in the database. I want to use the allelic sequence from the sample. Will it be possible to tweak the tool or to use any existing option so that we can also have 7 gene allele sequences extracted from the sample genome being analyzed. Looking forward for your valuable suggestion. Thanks

Nits11 commented 5 years ago

Please suggest your valuable input for my problem. Thanks

tseemann commented 5 years ago

There is a --novel OUTFILE option - does that do what you want?

Ivalize commented 5 years ago

Hi.

I have the same question. How to generate a fasta sequence file with the allelic detection (output file with the sequence aligned) ?.

Thanks.

tseemann commented 5 years ago

@Ivalize sequence aligned to the reference? can you describe in more detail what you would like?