Releases: metagenlab/diag_pipelines
Releases · metagenlab/diag_pipelines
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
2.5.0
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
2.3.1
- updated prokka
- updated Walker MTB database
2.3.0
- Changed sample sheet format: paths to fastq files can now be reported in the sample sheet (columns R1 and R2). The "links" folder is not needed anymore.