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bcbio-nextgen: Automated, distributed next-gen sequencing pipeline


 
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1. Title Title of document bcbio-nextgen: Automated, distributed next-gen sequencing pipeline
 
2. Creator Author's name, affiliation, country Roman Valls Guimera; , Science for life genomics staff, Brad Chapman* Harvard School of Public Health, Bioinformatics Core;; Sweden
 
3. Subject Discipline(s)
 
3. Subject Keyword(s) next generation sequencing; COST; python; LSF; SGE; SLURM framework
 
4. Description Abstract

http://www.hsph.harvard.edu/research/bioinfocore/
http://www.scilifelab.se/


bcbio-nextgen is an Python framework for next generation sequencing analysis. The fully automated pipeline interacts with the sequencing machine, runs sequences through configurable processing pipelines, and uploads the data into Galaxy for visualization and additional processing. The variant calling analysis pipeline handles alignment to a reference genome, variant identification with GATK and preparation of summary PDF files for assessing run quality.


The pipeline is fully distributed and will run on single multicore machines or in compute clusters managed by LSF, SGE or SLURM. The CloudBioLinux and CloudMan projects utilize this pipeline for distributed analysis on Amazon cloud infrastructure.


The Galaxy web-based analysis tool can be optionally integrated with the analysis scripts. 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.


Relevant Web sites
1. http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/
2. http://bcbio.wordpress.com/2011/09/10/parallel-approaches-in-next-generation-sequencing-analysis-pipelines/
3. https://github.com/brainstorm/bcbb/tree/master/nextgen
4. http://www.slideshare.net/chapmanb/developing-distributed-analysis-pipelines-with-shared-community-resources-using-cloudbiolinux-and-cloudman
 
5. Publisher Organizing agency, location EMBnet
 
6. Contributor Sponsor(s)
 
7. Date (YYYY-MM-DD) 28-Feb-2012
 
8. Type Status & genre Peer-reviewed Article
 
8. Type Type
 
9. Format File format PDF
 
10. Identifier Uniform Resource Identifier https://journal.embnet.org/index.php/embnetjournal/article/view/286
 
10. Identifier Digital Object Identifier (DOI) https://doi.org/10.14806/ej.17.B.286
 
11. Source Title; vol., no. (year) EMBnet.journal; Vol 17: Supplement B
 
12. Language English=en
 
14. Coverage Geo-spatial location, chronological period, research sample (gender, age, etc.)
 
15. Rights Copyright and permissions Copyright (c)