diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e991fe..761372d 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,11 @@ # 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 diff --git a/README.md b/README.md index 082daf9..3be9cdc 100755 --- a/README.md +++ b/README.md @@ -64,11 +64,11 @@ To create a conda environment named `btyper3` and install BTyper3 and all of its ------------------------------------------------------------------------ -## News: updates in BTyper3 v3.2.0 and v3.3.0 -- new species just dropped! +## News: updates in BTyper3 v3.2.0, v3.3.0, and v3.4.0 -- new species just dropped! The primary function of BTyper3 is to allow users to taxonomically classify *B. cereus* group genomes using a standardized nomenclature (see here and here for details regarding how the standardized nomenclature was constructed, and how it compares to historical typing methods, respectively). However, we understand that some users may also want to compare their *B. cereus* group genomes to the type strain genomes of published *B. cereus* group species. Thus, in BTyper3 v3.2.0, we have added the `--ani_typestrains` option, which calculates ANI values between a 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. -The type strain genomes used by BTyper3's `--ani_typestrains` option correspond to the species discussed in Figure 2 of our taxonomy review, plus five species published after the review was published (i.e., *Bacillus sanguinis*, *Bacillus paramobilis*, and *Bacillus hominis*, added in v3.2.0, and "*B. arachidis*" and *B. rhizoplanae*, added in v3.3.0). Within the standardized taxonomy that BTyper3 uses for genomospecies assignment: +The type strain genomes used by BTyper3's `--ani_typestrains` option correspond to the species discussed in Figure 2 of our taxonomy review, plus species published after the review was published (i.e., *Bacillus sanguinis*, *Bacillus paramobilis*, and *Bacillus hominis*, added in v3.2.0; "*B. arachidis*" and *B. rhizoplanae*, added in v3.3.0; "*B. pretiosus*", added in v3.4.0). Within the standardized taxonomy that BTyper3 uses for genomospecies assignment: * All members of *Bacillus sanguinis* (type strain RefSeq Assembly Accession GCF_018332475.1) belong to *B. mosaicus* (i.e., *B. sanguinis* is not considered a novel species in the standardized taxonomy) @@ -80,6 +80,8 @@ The type strain genomes used by BTyper3's `--ani_typestrains` option correspond * *Bacillus rhizoplanae* (type strain RefSeq Assembly Accession GCF_917563915.1) represents a novel genomospecies within the standardized taxonomy and has been added to the database +* All members of "*Bacillus pretiosus*" (type strain RefSeq Assembly Accession GCF_025916425.1) belong to *B. mosaicus* (i.e., "*B. pretiosus*" is not considered a novel species in the standardized taxonomy) + **Importantly, *B. cereus* group species are often proposed in the literature using unstandardized approaches** (e.g., varying genomospecies thresholds, which may produce overlapping genomospecies). We have added the type strain comparison method in BTyper3 v3.2.0, as users may still want to compare a query genome with the type strains of published *B. cereus* group species. However, interpret results with caution, as some *B. cereus* group genomes may belong to multiple species using type strain genomes. For more information, check out our: @@ -131,28 +133,28 @@ btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory --fastani_path /path/to/FastANI_executable/fastANI ``` -#### Perform all default analyses, plus pseudo-gene flow unit assignment AND species type strain comparison, using an assembled genome (complete or draft) in (multi-)FASTA format as input (assumes fastANI is in the user's path): +#### Perform all default analyses, plus pseudo-gene flow unit assignment, using an assembled genome (complete or draft) in (multi-)FASTA format as input (assumes fastANI is in the user's path): ``` -btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory --ani_geneflow True --ani_typestrains True +btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory --ani_geneflow True ``` #### Perform seven-gene MLST only, using user-supplied MLST gene sequences and the latest version of the PubMLST *B. cereus s.l.* database (sequences can be in multi-FASTA format, or concatenated into a single sequence in FASTA format): ``` -btyper3 -i /path/to/mlst.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --virulence False --bt False --panC False --download_mlst_latest True +btyper3 -i /path/to/mlst.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --ani_typestrains False --virulence False --bt False --panC False --download_mlst_latest True ``` #### Perform *panC* group assignment only, using a user-supplied *panC* gene sequence in FASTA format: ``` -btyper3 -i /path/to/panC.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --virulence False --bt False --mlst False +btyper3 -i /path/to/panC.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --ani_typestrains False --virulence False --bt False --mlst False ``` #### Perform virulence factor and Bt toxin-encoding gene detection in a plasmid sequence in FASTA format: ``` -btyper3 -i /path/to/plasmid.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --mlst False --panC False +btyper3 -i /path/to/plasmid.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --ani_typestrains False --mlst False --panC False ``` diff --git a/btyper3/__init__.py b/btyper3/__init__.py index ebd69ba..7e0e248 100755 --- a/btyper3/__init__.py +++ b/btyper3/__init__.py @@ -21,7 +21,7 @@ from .print_final_results import FinalResults __author__ = "Laura M. Carroll " -__version__ = "3.3.4" +__version__ = "3.4.0" @contextlib.contextmanager