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Create MLST Scheme tool leads to strains being linked to wrong sequence type in some cases

Issue description

The “Create MLST Scheme” tool in affected software versions associates sequences with alleles based on the position of each sequence in the list of those selected. This means that sequences will be associated with the correct allele type only if

Otherwise, the association of sequence types with alleles will be incorrect.

Tools that download and import schemes directly from public sites like PubMLST are not affected by this issue, specifically the “Download MLST Schemes (PubMLST) and “Download Other MLST Scheme” tools provided by the CLC Microbial Genomics Module and the CLC MLST Module.

Expected impact and recommendations


We expect many MLST schemes created using “Create MLST Scheme”, where sequences have been added to genes in the profile, to be affected when using the software listed below. Where an affected scheme is being used, in affected software versions or later software versions, isolates types are likely to be associated with the wrong sequence type.


If an MLST scheme was created using an affected software version (see below), and sequences were added to genes, we recommend checking that:

This can be done by opening the scheme and going to the Allele Table view. If you find your MLST scheme is affected by this problem, please discard the scheme and disregard the sequence types in any results that have been generated using it.

New schemes, unaffected by this problem, may be set up in one of the following ways:

Affected software and versions

This issue was addressed in CLC Microbial Genomics Module 4.8 and CLC MLST Module  1.9.2.