A coverage analysis package for clinical sequencing.
Project description
Chanjo (Swahili, lit. vaccine) is a sane coverage analysis tool focusing on clinical sequencing. It aims to simplify answering clinically relevant questions like: how well is my gene of interest covered?.
$ chanjo annotate db.sqlite using test.bam EGFR ALB CD4 BRCA1 --sample "fancy_sample_id"
$ chanjo peak db.sqlite EGFR
{
"EGFR": [
{
"sample": "fancy_sample_id",
"completeness": 1.0,
"coverage": 227.64
}
]
}Are you more interested in the Python API? Check out the official documentation.
Introduction
Verifying adequate read coverage is an important task to ensure robustness in clinical sequencing. Enabling this in collaboration with clinicians demand new software developed with physicians rather than researchers in mind.
Alternative tools often hide intuitive genetic concepts such as genes, transcripts, and exons behind more fundamental, less descriptive abstractions. When it comes to the most well defined genetic elements, this can be likened to requiring knowledge of programming to use a computer.
Chanjo reads coverage directly from a BAM alignment making it a good fit in most bioinformatic pipelines. A portable yet powerful SQLite database consolidates the output. The ambitions is to create a standardized API for coverage across the exome.
Completeness (NEW)
The completeness metric is one concrete new feature you will get for free using Chanjo. It’s meant as a complement to average coverage as a measure of the success of coverage.
Completeness works as such. Decide on a cutoff “X” representing the lower limit of adequate coverage (e.g. 10x reads). Completeness is simply the percentage of bases across an element/interval that with coverage >= X.
I believe completeness to be a more useful assessment of coverage success than average coverage for at least many clinical purposes.
Contribute
Test and submit issues. Learn more and point out shortcomings in the extended documentation. For more details I’ll try to keep issues and milestones up-to-date as a source of what needs to be worked on.
Contributors
Robin Andeer
License
MIT
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