6.0.3

• adds hit coordinates to the start and end of gene coordinates
• adds antibiotics to the tab-separated output file
• switch to using GitHub actions for testing
• adds BLAST config file

6.0.2

• Adds support for Pyrodigal
• Adds new CARD 2023 citation

6.0.1

• Fixed kmer query failed to parse BAM file issue
• Fixed infinite loop if the FASTA file is empty
• Updated cleaned files and auto load print statements

6.0.0

• Added an option (--keep) to keep Prodigal CDS when used with --clean
• Removed option --exclude_nudge and replaced with --include_nudge
• Added options to use all CARD models with rgi bwt, by default rgi bwt use homolog models only
• Added dask and replace some os.system calls to improve performance
• Consensus sequences are reported at depth of at least 5 when using rgi bwt with KMA
• Updated rgi load and rgi auto_load commands

5.2.1

• Updated biopython to 1.78 and lxml to 4.6.5
• Updated READMEs and CITATIONS
• Updated hardcoded paths to be configurable
• Fixed channel order

5.2.0

• Added workflow to publish docker images automatically
• Added a workaround for failing certificates verification when downloading CARD data
• Updated and cleanup README
• Added a new feature to automatically load CARD databases into RGI, termed rgi auto_load
• Added kma aligner as default for rgi bwt as it shows better alignments over bowtie2 and bwa
• Updated RGI bwt read mapping results at allele level report (output_prefix.allele_mapping_data.txt) to include depth, SNPs, Consensus Sequence DNA, Consensus Sequence Protein
• Added support for gz and bz2 input FASTA for rgi main
• rgi bwt now uses homolog, variant, rRNA gene variant, overexpression, and knockout models

5.1.1

fixed index error with rRNA models
fixed index for bwa and added kma aligner for rgi bwt
supports BLAST version to 2.9.0
catch unset SNP parameters

5.1.0

• added beta version for K-mer taxonomic classifiers (rgi kmer_build and rgi kmer_query)
• updated the code to accept a broader range of nucleotide redundancy codes
• set biopython to version 1.72 due to bug on biopython version 1.74

5.0.0

• added rgi bwt module for predicting AMR determinants in metagenomics
• updated documentation
• added a flag for nudged hits from loose to strict
• added support for partial sequences

4.2.2

• fixes indexing error