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tseemann / legsta

🍗⭐ In silico Legionella pneumophila Sequence Based Typing
GNU General Public License v3.0
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flaA allele 11 not detected #15

Open marithetland opened 3 years ago

marithetland commented 3 years ago

Hi, thanks for making this tool, it's very useful! I am running it on 70 genomes which I also have Sanger SBT on to compare. For most of the genomes, legsta finds the same SBT, but it does not seem to find flaA allele 11. 25 of the genomes (SBTs 154 and 574) should have flaA 11, but legsta outputs "-" for this allele. Other flaA alleles are found in the other genomes. When I run BLASTn on the assemblies using the flaA 11 sequence from https://github.com/tseemann/legsta/blob/master/db/flaA.tfa, I find flaA_11 with 100% nucleotide identity and sequence coverage.

Also, for 12 of those 25 genomes, the mompS-gene was called incorrectly (as allele 7 in stead of 15). The mompS-allele is correctly called in all the other genomes I have looked at.

Any idea what is going on?

Thanks, Marit

Julio92-C commented 2 years ago

@marithetland, I have the same issue. Any idea how can I solve it?