CHANGELOG.md

BTyper3 CHANGELOG

All notable changes to BTyper3 will be documented in this file.

[3.4.0] - 2023-06-01

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] - 2022-12-13

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] - 2022-10-17

Fixed

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

[3.3.2] - 2022-08-20

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] - 2022-08-12

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] - 2022-08-11

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 database
• Included ndb, not, ntf, and nto in the list of BLAST database files to delete

[3.2.0] - 2021-04-12

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.

[3.1.2] - 2021-04-12

Changed

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

[3.1.1] - 2020-10-25

Added

• Added download_pubmlst_latest.py script, which users can run to download latest PubMLST database for Bacillus cereus, independently of executing the btyper3 program

Changed

• Updated --download_mlst_latest portion of btyper3 code to be compatible with changes to PubMLST's XML format; recent changes made by PubMLST to the filenames in the XML caused previous versions of BTyper3 to produce an error and not download the database

Removed

• Removed Unknown Species 14 from the species reference genomes used for genomospecies assignment; using recent genomes submitted to NCBI (accessed 2020-05-14), Unknown Species 14 was found to overlap with B. luti at a 92.5 ANI threshold (see genomes with NCBI RefSeq Assembly Accessions GCF_008764075.1, GCF_007667455.1, and GCF_007673665.1, which were assigned to both B. luti and Unknown Species 14 at a 92.5 ANI threshold); Unknown Species 14 was therefore merged into B. luti in BTyper3 v. 3.1.1

[3.1.0] - 2020-06-28

Added

• Added in silico seven-gene multi-locus sequence typing (MLST), using PubMLST's scheme for Bacillus cereus
• Added panC group assignment using an eight-group panC group assignment framework
• Added virulence factor detection for additional virulence factors (i.e., toxin genes associated with diarrheal Bacillus cereus illness, and genes associated with capsule production)
• Added average-nucleotide identity (ANI)-based pseudo-gene flow unit assignment method

Changed

• Changed default virulence factor detection thresholds to 70 and 80% amino acid identity and coverage, respectively

[3.0.2] - 2019-11-18

Changed

• Swapped anthrax and cereulide column names in final results file (previously, the column header for anthrax genes was above cereulide synthetase genes in the final results file, and vice versa; the typo was thus fixed)
• Edited the README to convey that BLAST+ version 2.10.0 is not compatible with BTyper3

[3.0.1] - 2019-10-05

Changed

• Changed default percent amino acid identity for virulence gene detection and Bt toxin gene detection from 70% to 50% to be compatible with what was reported in the preprint
• Fixed pandas.read_csv error which would occur when no fastANI and/or BLAST output file would be produced, or when a file was empty
• Fixed error which would occur when printing final output files when --virulence False or --bt False; when these typing methods were not performed, the final output file would treat the string which designated that these typing methods were not performed as a list

[3.0.0] - 2019-09-22

Added

• Initial commit of BTyper3