Best-practice pipelines for fully automated high throughput sequencing analysis
Project description
bcbio-nextgen
A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input 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 handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
The advantages of a community developed framework over in house custom scripts include:
Automated validation of variant calls against common reference materials or sample specific SNP arrays to ensure call correctness.
Focus on parallel analysis and scaling to handle large population studies and whole genome analysis.
Incorporation of multiple approaches for alignment, preparation and variant calling enable unbiased comparisons of algorithms.
Quick start
Install bcbio-nextgen with all tool dependencies and data files:
wget https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py python bcbio_nextgen_install.py /usr/local /usr/local/share/bcbio-nextgen
producing a system configuration file referencing the installed software and data.
Create a sample configuration file for your samples:
bcbio_nextgen.py -w template gatk-variant project1 sample1.bam sample2_1.fq sample2_2.fq
Run analysis, distributed across 8 local cores:
bcbio_nextgen.py bcbio_system.yaml bcbio_sample.yaml -n 8
Documentation
See the full documentation at ReadTheDocs. We welcome enhancements or problem reports using GitHub and discussion on the biovalidation mailing list.
Pipelines
Variant calling
bcbio-nextgen implements configurable best-practice pipelines for SNP and small indel calling:
Sequence alignment:
Base Quality Recalibration
Realignment around indels
Variant calling:
GATK Unified Genotyper (supports both GATK-lite in GATK 2.3 and commercial restricted version in GATK 2.4+)
GATK Haplotype caller (part of the commercially restricted GATK 2.4+)
Quality filtering, using either GATK’s Variant Quality Score Recalibrator or hard filtering.
Annotation of variant effects, using snpEff
Variant exploration and prioritization, using GEMINI
It follows approaches from:
GATK best practice guidelines for variant calling
Marth Lab’s gkno pipelines
Features
Distributed
The pipeline runs on single multicore machines, in compute clusters managed by LSF or SGE using IPython parallel, or on the Amazon cloud. This tutorial describes running the pipeline on Amazon with CloudBioLinux and CloudMan.
Galaxy integration
The scripts can be tightly integrated with the Galaxy web-based analysis tool. Tracking of samples occurs via a web based LIMS system, and processed results are uploading into Galaxy Data Libraries for researcher access and additional analysis. See the installation instructions for the front end and a detailed description of the full system.
Contributors
Guillermo Carrasco, Science for Life Laboratory, Stockholm
Brad Chapman, Harvard School of Public Health
Peter Cock, The James Hutton Institute
Rory Kirchner, Harvard School of Public Health
Brent Pedersen, University of Colorado Denver
Valentine Svensson, Science for Life Laboratory, Stockholm
Roman Valls, Science for Life Laboratory, Stockholm
License
The code is freely available under the MIT license.
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