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Maintenance and Improvement of Validated, Community Developed NGS Analyses

Project bcbio-nextgen

Rory Kirchner (Harvard Chan School of Public Health)

Funding Cycle 1

Proposal Summary

To improve the bcbio-nextgen toolkit, focusing on maintaining existing variant calling functionality and extending support for structural and RNA-seq variant analyses.



bcbio-nextgen is a Python toolkit providing best practice pipelines for fully-automated high throughput sequencing analysis. The user writes a high level configuration file specifying inputs and analysis parameters, which drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that automates the data processing component of sequencing analysis via validated, current, best practice methods, providing researchers with more time to focus on the downstream biology. bcbio-nextgen is installable for users on any UNIX-based environment without administration privileges and installs all of the tools and data needed to run a wide variety of different NGS analyses. bcbio-nextgen is scalable and agnostic to the underlying compute infrastructure— it can run on a local machine, in HPC environments with support for all cluster schedulers and runs on cloud providers such as Amazon Web Services (AWS), Google Cloud (GCP) and Microsoft Azure.

Key Personnel

Rory Kirchner
Sergey Naumenko