rgi - 6.0.5

• Updated to write .ncbirc config once
• Added AST_Source column for mutations
• Fixed contig column and regex typo
• Switched to handling nucleotides snps in lowercase

- Python
Published by raphenya 11 months ago

rgi - 6.0.4

• Updated versions used for BLAST, Pyrodigal, KMA, samtools, and libs
• Support for Var and Ter mutations
• Fixed Runtime Error
• Added more tests

- Python
Published by raphenya about 1 year ago

rgi - 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

- Python
Published by raphenya over 2 years ago

rgi - 6.0.2

• Adds support for Pyrodigal
• Adds new CARD 2023 citation

- Python
Published by raphenya about 3 years ago

rgi - 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

- Python
Published by raphenya over 3 years ago

rgi - 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

- Python
Published by raphenya over 3 years ago

rgi - 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

- Python
Published by raphenya about 4 years ago

rgi - 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 (outputprefix.allelemapping_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

- Python
Published by raphenya almost 5 years ago

rgi - 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

- Python
Published by raphenya almost 6 years ago

rgi - 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

- Python
Published by raphenya over 6 years ago

rgi - 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

- Python
Published by raphenya almost 7 years ago

rgi - 4.2.2

• fixes indexing error

- Python
Published by arpcard over 7 years ago

rgi - 4.2.1

• Updated output json to include possible start and stop missed by Prodigal v2.6.3
• Added tests for heatmap

- Python
Published by arpcard over 7 years ago

rgi - 4.2.0

• added heatmap to compare multiple rgi json outputs
• updated documentation with examples for using heatmap
• fixed minor bugs which include missing keys, imports and string comparison

- Python
Published by arpcard over 7 years ago

rgi - 4.1.0

• fixed bug with mutation

- Python
Published by arpcard over 7 years ago

rgi - 4.0.3

• updated LICENSE
• minor fixes

- Python
Published by raphenya almost 8 years ago

rgi - 4.02

• Added support for docker
• Added flag (--low_quality) to predict partial genes from short contigs
• Updated dependencies
• Added --debug flag

- Python
Published by arpcard about 8 years ago

rgi - 4.0.1

• added support to store database in the working directory by using --local flag
• --local flag added to rgi subcommands: main, load, clean and database

- Python
Published by arpcard about 8 years ago

rgi - 4.0.0 Object Oriented

• Updated menu
• Compatible with CARD data (card.json) version 2.0.0 and up
• CARD data (card.json) has to be downloaded from CARD before using the software
• RGI results are classified using Drug Class, Resistance Mechanism and AMR Gene Family

- Python
Published by raphenya about 8 years ago

rgi -

- Python
Published by raphenya over 8 years ago