3.4.0

Added

• Added "Bacillus pretiosus" (NCBI RefSeq Assembly Accession GCF_025916425.1) to the --ani_typestrains database

Changed

• Changed --ani_typestrains to True by default (to be compatible with BRisk USDA project)

3.3.4

Fixed

• btyper3.ani occasionally crashing in --ani_geneflow when the best hit is under threshold and not enough hits were obtained.

Changed

• Reorganize btyper3.ani data files to store metadata and rewrite formatting code in Ani.run_fastani.

3.3.3

Fixed

• btyper3.ani failing to read query genome from an exhausted sequence iterator.

3.3.2

Fixed

• PyFastANI result handling code crashing on genomes too distant from the database genomes.

Added

• Warning when running btyper3 on a very fragmented genome.

3.3.1

Fixed

• Issue with PyFastANI migration when running the --ani_geneflow and --ani_typestrains operations.
• Wrong program name being shown when running btyper3 in module form (python -m btyper3).

3.3.0

Added

• Added "Bacillus arachidis" (NCBI RefSeq Assembly Accession GCF_017498775.1) to the --ani_typestrains database
• Added Bacillus rhizoplanae (NCBI RefSeq Assembly Accession GCF_917563915.1) to the --ani_typestrains and --ani_species databases

Changed

• Changed the name of "Unknown Species 17" to "Bacillus arachidis" in the --ani_species databasie
• Included ndb, not, ntf, and nto in the list of BLAST database files to delete

BTyper3 v3.2.0

Added

• Added --ani_typestrains option to btyper3, which allows users to compare a query B. cereus group genome to the type strain genomes of all published B. cereus group species in the literature; this options calculates ANI values between the query genome and the genomes of all published B. cereus group species type strains and reports the type strain that produces the highest ANI value.
• Added typestrains-only database to build_btyper3_ani_db.py, which allows users to download the type strain genomes of all published B. cereus group species; this database is used with the --ani_typestrains in btyper3. Type strain genomes correspond to the species discussed in Figure 2 of our taxonomy review, plus three species published after the review was published.
• See the BTyper3 changelog for more details regarding previous BTyper3 versions

BTyper3 v3.1.2

Changed

• Fixed typo in download_pubmlst_latest.py so that xml could properly parse the PubMLST xml

See the BTyper3 changelog for more details regarding previous BTyper3 versions

BTyper3 v3.1.1

The BTyper3 release described in the BTyper3 paper

See the BTyper3 archive and Changelog for information regarding releases prior to 3.1.1