# Cpipe: a shared variant detection pipeline designed for diagnostic settings

## TL;DR

Cpipe is a new open-source pipeline for clinical genomics that offers fast, flexible, and reproducible analysis for genetic disease diagnostics.

## Contribution

Cpipe is a novel, freely available bioinformatics pipeline specifically designed for clinical genomics diagnostics.

## Key findings

- Cpipe was developed to meet the needs of diverse clinical settings with flexibility and customizability.
- The pipeline is being shared as an open-source project to support clinical sequencing efforts.

## Abstract

The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines have been built from the ground up with clinical genomics in mind. Here we present Cpipe, a pipeline designed specifically for clinical genetic disease diagnostics. Cpipe was developed by the Melbourne Genomics Health Alliance, an Australian initiative to promote common approaches to genomics across healthcare institutions. As such, Cpipe has been designed to provide fast, effective and reproducible analysis, while also being highly flexible and customisable to meet the individual needs of diverse clinical settings. Cpipe is being shared with the clinical sequencing community as an open source project and is available at http://cpipeline.org.

The online version of this article (doi:10.1186/s13073-015-0191-x) contains supplementary material, which is available to authorized users.