StxTyper 1.0.40

Extensive testing on real data identified some rare cases with non-optimal calls in incomplete stx operons that led us to revise the algorithm slightly. These changes should have no effect on the stx_type returned by StxTyper and no effect on results for complete operons.

Differences from release version 1.0.27 are:

• We added a --threads option to speed blast searches.
• Added an 80% amino-acid identity cutoff for subunit calls and an 80% identity cutoff for the operon as a whole.
• Set gap extension penalty (--gapextend 2) in blast parameters to avoid unusual alignments with excess indels. This fixed some poor quality hits returned in rare cases.
• In AMRFinderPlus output format operons will now have qualifiers added to the name like "Partial" or "Novel" to make it clear that these are not operons that can be fully typed to the subtype level.

StxTyper 1.0.31

This release only changes the format of the AMRFinderPlus compatible output of StxTyper (--amrfinder option). It does not change StxTyper results from the previously released version 1.0.27. You do not need to update to this version if you are running StxTyper alone, and a new version of AMRFinderPlus (4.0.15) will be released that includes these changes.

• Empty fields are now filled with 'NA'
• Commas are removed from the Closest reference accession field

No change to the algorithm or results.

StxTyper 1.0.27

This release has a few more minor changes that change the --amrfinder output as part of its inclusion with AMRFinderPlus version 4.0.3. The typing database and algorithm are unchanged.

• The column "Element length" in --amrfinder output was renamed back to "Target length" for clarity
• --print_node output with mixed types is :: E.g., stxA2c::stxB2a

StxTyper 1.0.25

This is a release that primarily differs from version 1.0.24 in that it has changed column headers for the --amrfinder output format. This is in preparation to release a version of AMRFinderPlus that includes this software as part of its pipeline.

StxTyper 1.0.24

StxTyper 1.0.24

First public release for testing. Please open a ticket if you see any issues or have any suggestions. Comments on documentation or the installation process are also welcome.