Jasentool

Multipurpose tool for jobs related to the JASEN pipeline and Bonsai.

Subcommands

Post-run analysis

Subcommand	Description
`find`	Query samples from MongoDB
`identify-missing`	Identify samples absent from JASEN results directory
`validate-pipelines`	Compare pipeline outputs against MongoDB records

Pipeline processes

Subcommand	Description
`annotate-delly`	Annotate Delly structural-variant VCFs with gene symbols and locus tags
`concatenate-files`	Concatenate multiple YAML files
`count-reads`	Count reads in FASTQ file(s)
`create-blacklist`	Aggregate minority base frequencies across BAMs to produce a blacklist TSV
`create-yaml`	Create YAML input file for Bonsai upload
`minority-report`	Compute minority base frequency distribution from a samtools mpileup file
`post-align-qc`	Compute post-alignment QC from BAM

Site-specific hooks

Subcommand	Description
`reformat-csv`	Reformat BJORN CSV/SH files for JASEN

Setup & reference data

Subcommand	Description
`converge-catalogues`	Merge WHO, TBdb, and FoHM TB mutation catalogues
`download-bigsdb`	Download cgMLST scheme alleles from PubMLST or BIGSdb
`download-ncbi`	Download genome FASTA and GFF from NCBI
`transform-file-format`	Convert cgMLST target TSV to BED format

Quick Start

pip install jasentool

Query samples from MongoDB

jasentool find \
  --query MySampleID \
  --db-name mydb \
  --db-collection samples \
  --output-file results.json

Identify missing samples

jasentool identify-missing \
  --output-file missing.json \
  --db-name mydb \
  --db-collection samples \
  --analysis-dir /path/to/jasen/results

Validate pipeline outputs

jasentool validate-pipelines \
  --input-dir /path/to/new/results \
  --output-dir /path/to/validation/output \
  --db-name mydb \
  --db-collection samples

See Installation and Usage for full details.