Kleborate v2.1.0

Changes since v2.0.4 include:

• Updated chromosomal MLST alleles/profiles
• Updated virulence MLST alleles/profiles
• Updated species classification database
• When a virulence locus contains any truncated genes, (truncated) will be appended to the lineage/element

Kleborate v2.0.4

Two changes in this version:

• There is now a minimum threshold for Kaptive confidence, below which loci will be reported as 'unknown'.

  • For example, if Kaptive found a best K locus of KL102 but with a confidence of None, it will now be reported as unknown (best match = KL102) in Kleborate.
  • The default minimum confidence level is 'Good' and this can be changed with Kleborate's new --min_kaptive_confidence setting.

• We made some cosmetic changes to the help text, including the display of default values for settings.

Kleborate v2.0.3

For this version of Kleborate, we changed the internal logic for how exact amino acid matches are called:

• Previously, we used tblastx to align the assembly's gene sequence to reference alleles, looking for an exact match. However, some cases popped up where this wasn't working due to bizarre BLAST behaviour.
• Now, we use Biopython to translate the assembly's gene sequence and the reference alleles, and then look for a match in the translate sequences. This seems more robust!

Additionally we fixed a bug that occurred in an annoying corner-case:

• Previously, if an allele had a mutated start/stop codon, exact amino acid matches could be missed. This happened because a change at the very start/end of the gene sequence would result in a not-quite-full-length nucleotide match.
• Now, mutated start/stop codons can still give the appropriate exact amino acid match.

Kleborate v2.0.1

Two bug fixes in this release:

• Kleborate now runs Kaptive with the same Python interpreter it's using. Fixes a crash that could happen if you didn't have python3 in your PATH. Thanks, @EricDeveaud!
• The SHV-56 allele was described inconsistently in the FASTA and CSV files, which could cause a crash. Now fixed!

Kleborate v2.0.0

Tons of changes in this version! Highlights include:

• Improved gene databases
• Improved logic for choosing between alternative alleles
• Added assembly stats: total size, number of ambiguous bases and QC warnings
• New command line options to control coverage and identity thresholds
• Improved resistance gene/class counts'
• Added rmpADC as a virulence locus
• Allowed multiple results per genome for virulence loci
• Added new columns for spurious/truncated hits
• Renamed resistance columns to include 'acquired' or 'mutations' for clarity
• Reorganised Bla classes
• Check for SHV mutations
• Lots of improvements to the resistance gene database

See the full documentation in the Kleborate wiki for more information!

Kleborate v1.0.0

Major changes in this version - see readme for more details.

Highlights include:

• Kleborate is now Python 3 only, and makes clear that Biopython is a requirement.
• Added unit tests - see /test directory.
• Added newly defined Klebs species.
• Updated MLST database (as at 8 Oct 2019).
• Added helper script added to allow users to upload the MLST database on demand.
• Added OmpK35 and OmpK36 mutation detected (new column 'Omp' in output).
• Resistance gene logic was updated to check for exact protein match if exact nt match is not found.
• AMR gene database updated, including new tetX gene for tigecycline resistance which is not reported in its own column 'Tgc'.
• 'hypermucoidy' column is replaced by separate 'rmpA' and 'rmpA2' columns, which include checking/reporting for truncation of the encoded products and prediction of location of the gene.
• Added helper script to format Kleborate output files for viewing in microreact.
• Some versions/platforms of BLAST can crash when running with multiple threads. If Kleborate encounters this crash when running Kaptive, it will automatically retry with a single thread (slower but avoids the crash).

Kleborate v0.3.0

This release includes updated analyses of aerobactin and salmochelin, to accompany the paper on these loci (Lam et al 2018); and rmpA and rmpA2 subtyping.

NOTE that aerobactin and salmochelin lineage names have been updated since v0.2.0, to reflect the rationalised nomenclature established in the paper. The relevant sequence types (AbST, SmST) are unchanged between versions and a mapping of old to new lineage names is given in the readme.

Kleborate v0.2.0

The first release of Kleborate!