bcbio-nextgen：这个工具箱为全自动高通量测序分析提供符合最佳实践的处理流程

bcbio-nextgen：这个工具箱为全自动高通量测序分析提供符合最佳实践的处理流程

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel run that handles distributed execution, idempotent processing restarts and safe transactional steps. bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.

Features

Community developed: We welcome contributors with the goal of overcoming the biological, algorithmic and computational challenges that face individual developers working on complex pipelines in quickly changing research areas. See our users page for examples of bcbio-nextgen deployments, and the developer documentation for tips on contributing.Installation: A single installer script prepares all third party software, data libraries and system configuration files.Automated validation: Compare variant calls against common reference materials or sample specific SNP arrays to ensure call correctness. Incorporation of multiple approaches for alignment, preparation and variant calling enable unbiased comparisons of algorithms.Distributed: Focus on parallel analysis and scaling to handle large population studies and whole genome analysis. Runs on single multicore computers, in compute clusters using Ipython parallel, or on the Amazon cloud. See the parallel documentation for full details.Multiple analysis algorithms: bcbio-nextgen provides configurable variant calling, RNA-seq and small RNA pipelines.

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.pypython bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local \ --genomes GRCh37 --aligners bwa --aligners bowtie2 producing an editable system configuration file referencing the installed software, data and system information. Automatically create a processing description of sample FASTQ and BAM files from your project, and a CSV file of sample metadata: bcbio_nextgen.py -w template freebayes-variant project1.csv sample1.bam sample2_1.fq sample2_2.fq This produces a sample description file containing pipeline configuration options. Run analysis, distributed across 8 local cores: cd project1/workbcbio_nextgen.py ../config/project1.yaml -n 8

Documentation

See the full documentation and longer analysis-based articles. We welcome enhancements or problem reports using GitHub and discussion on the biovalidation mailing list.

Contributors

Miika Ahdesmaki, AstraZenecaLuca Beltrame, IRCCS "Mario Negri" Institute for Pharmacological Research, Milan, ItalyChristian Brueffer, Lund University, Lund, SwedenAlla Bushoy, AstraZenecaGuillermo Carrasco, Science for Life Laboratory, StockholmNick Carriero, Simons FoundationBrad Chapman, Harvard Chan Bioinformatics CoreSaket Choudhary, University Of Southern CaliforniaPeter Cock, The James Hutton InstituteMatt Edwards, MITMario Giovacchini, Science for Life Laboratory, StockholmKarl Gutwin, BiogenJeff Hammerbacher, Icahn School of Medicine at Mount SinaiOliver Hofmann, Wolfson Wohl Cancer Research CenterJohn KernRory Kirchner, Harvard Chan Bioinformatics CoreJakub Nowacki, AstraZenecaJohn Morrissey, Harvard Chan Bioinformatics CoreLorena Pantano, Harvard Chan Bioinformatics CoreBrent Pedersen, University of Colorado DenverJames Porter, The University of ChicagoValentine Svensson, Science for Life Laboratory, StockholmPaul Tang, UCSFRoman Valls, Science for Life Laboratory, StockholmKevin Ying, Garvan Institute of Medical Research, Sydney, AustraliaVlad Saveliev, Center for Algorithmic Biotechnology, St. Petersburg University

License

The code is freely available under the MIT license.

版权声明：本文内容由网络用户投稿，版权归原作者所有，本站不拥有其著作权，亦不承担相应法律责任。如果您发现本站中有涉嫌抄袭或描述失实的内容，请联系我们jiasou666@gmail.com 处理，核实后本网站将在24小时内删除侵权内容。