2.8.3

Test zenodo link

2.8.2

New release to fix problems with rst reports, resistance reports and genome annotation with bakta

014201d : fix problem with very long lines in rst reports
b24c413, b24c413, 1d39c64: deal with genomes without resistance genes
718ba52: removed problematic "--complete" argument for bakta annotation

Updated contig filter

• updated low depth contigs filter: use a fraction of the mean depth rather than a fixed cutoff

2.7.0

• added platon for plasmid identification
• added bakta as alternative to prokka
• added aro filter for reports
• added stats assembly graph

2.6.0

• updated resistance workflow (combine data from BLDB and rgi for report)
• added gtdbtk for classification

2.5.2

• bug fix

2.5.1

• bug fixes

2.5.0

Added new QC to resistance workflow:

• extract 16S sequence and assign taxnonomy using Ezbiocloud database
• estimate contamination and completeness of genomes with checkM

2.4.1

• bug fixes
• report mutation for non synonymous SNPs

2.4.0

• update CARD/RGI to version 5.1.0-v3.0.8
• updated prokka version
• added tb-profiler