Welcome to Cpipe
New! : Cpipe is published in Genome Medicine!
Cpipe is an exome sequencing pipeline created by the Melbourne Genomics Health Alliane as part of a project to prototype clinical sequencing across multiple institutions in Australia. As part of the project, a pipeline was developed for analysis of exome and targeted sequencing data that is specialised for clinical purposes. Cpipe includes many features that are needed in clinical diagnostic settings, including:
- a full implementation of an industry standard variant calling pipeline
- automated, robust and highly parallelised using Bpipe
- clinical grade, detailed coverage reports at gene, exon and per base level
- a carefully designed variant prioritisation and curation system for ranking variants to bring clinically important variants to the top
- implemented in a highly customisable framework that lets you easily replace any given component or tune existing components to your needs
- A streamlined install process that gets you all the tools and reference data you need quickly and easily
- Self test system that checks critical clinical mutations are correctly identified
- Fully open source under a GPLv3 license with ongoing maintenance from the members of the Melbourne Genomics Health Alliance.