Chanjo2 documentation pages
Chanjo2 is coverage analysis tool for clinical sequencing data using the d4 (Dense Depth Data Dump) format. It's implemented in Python FastAPI and provides API endpoints to communicate with a d4tools software in order to return coverage and coverage completeness over genomic intervals (genes, transcripts, exons as well as custom intervals) over single d4 files or samples stored in the database with associated d4 files.
The tool is flexible and can be used in different ways. The simplest use case would be calculating sequencing coverage over one or more intervals for a d4 file stored locally or remotely on the internet.
Chanjo2 image as a proxy to d4tools to compute coverage stats over genomic intervals of a d4 file
Chanjo2 image contains d4tools and can be used to directly retrieve statistics over d4 files.
Executing d4tools
docker run --entrypoint d4tools --rm clinicalgenomics/chanjo2:latest
Calculating coverage on specific genomic intervals of a d4 file using d4tools
docker run --entrypoint d4tools --platform linux/x86_64 --rm -v <path-to-local-d4-files-folder>:/home/worker/infiles clinicalgenomics/chanjo2:latest view /home/worker/infiles/<d4file.d4> 1:1234560-1234580 X:1234560-1234580
Please note that the d4 file containing the coverage data can be also stored on a remote server. In this case the command above could be replaced by this one:
docker run --entrypoint d4tools --platform linux/x86_64 --rm clinicalgenomics/chanjo2:latest view <url-to-remote-d4-file.d4> 1:1234560-1234580 X:1234560-1234580
The coverage computation on a file hosted on a remote server, will be consistently slower than when hosting the file on a local server.
Chanjo2 as a REST server
When chanjo2 is launched and runs as a REST server, it is offering many additional features, including:
Support for calculating coverage and coverage completeness over genes, transcripts and exons for different genome builds- Chanjo2 server can be either installed on a virtual environment using poetry of directly launched using Docker
Instructions on how to set up and run Chanjo2 as a REST server as well as the functionalities that it offers are better illustrated in these dedicated pages.