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.

To get started, visit the Github page or have a look at the User Manual. Need help? Join our Google Group to talk about Cpipe with other users.