TBProfiler v4.3.0

Changes

New features

• Switch to jinja2 templating engine to produce text output. Also allows user to supply custom template with --output_template
• New function to list all loaded databases list_db
• Argument to prevent overwriting in create_db if db with same name already exists --no_overwrite
• New batch function to help batch run samples with a CSV as input
• Added spoligotype name annotations (#219)

Minor fixes

• Added spoligotype/rd information back into text report (#222)
• Fixed use of suspect api (#225)

TBProfiler v4.2.0

Changes

New features

• Experimental spoligotyping available (add --spoligotyping to profile command)
• Added some QC metrics to collate output (#205)
• Improved command line interface. All input file types can now be given on the to the main profile function (-1/-2: fastq, -a: bam/cram, -f: fasta, -v: vcf)

Fixes

• Fix for fasta profile (#208)

Other

• Removed pathogen-profiler code and put back into own repository (makes it easier to reuse that code for other profiling tools) https://github.com/jodyphelan/pathogen-profiler

TBProfiler v4.1.1

Change

• Fix for issue with itol output (#200)

TBProfiler v4.1.0

Updates

Thanks to everyone who submitted bug reports and suggested changes. Keep them coming :)

• Added pilon as a variant caller (#194)
• Added lofreq as a variant caller (#202)
• Updated the drug resistance types (#200)
• Update packaged db to latest version with mutations from WHO catalogue (see here)
• Fixed bug in snpEff call (#193)

TBProfiler v4.0.3

Changes

• Fixes for several bugs introduced in v4 (#187, #188 (thanks @pmenzel), #189, #190)
• Large deletions are now annotated using hgvs terminology, using gene coords (#191, jodyphelan/tbdb#21)

TBProfiler v4.0.2

Changes

• Remove temp file produced during pipeline run

TBProfiler v4.0.1

Changes

• Bug fix for critical bug introduced in v4.0.0 when installing with conda
• Update default caller to freebayes

TBProfiler v4.0.0

Changes

The json result files are formatted slightly differently from previous versions to accommodate the changes detailed below. As a consequence, operations such as collate will not work on results from previous versions.

• Switching to snpEff for consequence prediction for full HGVS compliance
• Optional use of suspect-BDQ and suspect-PZA for prediction of resistance
• Switching over to new Pre-XDR and XDR definitions (see WHO page)
• Allowing user-specified non drug resistance annotations (e.g. phylogenetic or compensatory mutations)
• Annotation of multiple consequences which is useful for overlapping promoter/coding regions
• Improvements in nanopore variant calling speed by moving to freebayes.
• Adding median coverage (#178)
• More flexible reference name matching when creating database
• Make freebayes the default variant caller
• Add some colour to terminal output!

TBProfiler v3.0.8

Changes

• Add in number of mutations to json report (#149)

TBProfiler v3.0.7

Changes

• Allow promoter insertions (#169)