I have applied mlst command to get the sequence type of a bunch of 155 assembly of klebsiella bacteria . It was successful in all of them except for 38 entry which did not reveal any ST although there was number assigned to the 7-genes. when I inspected the messages appeared in those negative ones, there was a warning saying: duplicate allele were also recovered in Klebsiella and E. coli. So, I took these assembly, and uploaded them on the center for genomic epidemiology (https://www.genomicepidemiology.org/services/), shere it gave me their ST. Could you please advice on how to tackle this in linux ? are there any other tool of mlst to retrieve the ST ?
this is was my code for some that did not reveal any ST:
mlst GCA_036986515.fasta
mlst GCF_004127345.fasta
mlst GCF_004127375.fasta
For some assemblies that gave a ST
mlst GCF_004127595.fasta
mlst GCF_004127885.fasta
