bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

https://github.com/bcbio/bcbio-nextgen

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
11 of 106 committers (10.4%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.4%) to scientific vocabulary

Keywords from Contributors

bioinformatics genomics quality-control nextflow workflow-engine workflows cwl pypi reporting seqera

Last synced: 7 months ago · JSON representation

Repository

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Basic Info

Host: GitHub
Owner: bcbio
License: mit
Language: Python
Default Branch: master
Homepage: https://bcbio-nextgen.readthedocs.io
Size: 41.4 MB

Statistics

Stars: 1,011
Watchers: 87
Forks: 355
Open Issues: 132
Releases: 14

Created about 13 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog License Code of conduct

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.

NOTE!!!! Please read the notice of discontinuation of this project - 08-16-2024

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 (small and copy number), RNA-seq, ATAC-seq, , BS-Seq, SC RNA-seq, and small RNA pipelines.

Quick start

Install bcbio-nextgen with all tool dependencies and data files: shell script wget https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local \ --genomes hg38 --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: shell script 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: shell script cd project1/work bcbio_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, AstraZeneca
Luca Beltrame, IRCCS "Mario Negri" Institute for Pharmacological Research, Milan, Italy
Christian Brueffer, Lund University, Lund, Sweden
Alla Bushoy, AstraZeneca
Guillermo Carrasco, Science for Life Laboratory, Stockholm
Nick Carriero, Simons Foundation
Brad Chapman, Harvard Chan Bioinformatics Core
Saket Choudhary, University Of Southern California
Peter Cock, The James Hutton Institute
Matthias De Smet, Center for Medical Genetics, Ghent University Hospital, Belgium
Matt Edwards, MIT
Mario Giovacchini, Science for Life Laboratory, Stockholm
Karl Gutwin, Biogen
Jeff Hammerbacher, Icahn School of Medicine at Mount Sinai
Oliver Hofmann, University of Melbourne Centre for Cancer Research
John Kern
Rory Kirchner, Harvard Chan Bioinformatics Core
Tetiana Khotiainsteva, Ardigen
Kerrin Mendler, AstraZeneca
Sergey Naumenko, Harvard Chan Bioinformatics Core
Jakub Nowacki, AstraZeneca
John Morrissey, Harvard Chan Bioinformatics Core
Lorena Pantano, Harvard Chan Bioinformatics Core
Brent Pedersen, University of Colorado Denver
James Porter, The University of Chicago
Vlad Saveliev, Center for Algorithmic Biotechnology, St. Petersburg University
Valentine Svensson, Science for Life Laboratory, Stockholm
Paul Tang, UCSF
Stephen Turner, University of Virginia
Roman Valls, Science for Life Laboratory, Stockholm
Kevin Ying, Garvan Institute of Medical Research, Sydney, Australia
Steffen Möller, University of Rostock, Germany
WimSpee

License

The code is freely available under the MIT license.

Owner

Name: Blue Collar Bioinformatics
Login: bcbio
Kind: organization

Website: http://bcb.io
Repositories: 18
Profile: https://github.com/bcbio

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

GitHub Events

Total

Issues event: 5
Watch event: 23
Issue comment event: 1
Fork event: 7

Last Year

Issues event: 5
Watch event: 23
Issue comment event: 1
Fork event: 7

Committers

Last synced: over 2 years ago

All Time

Total Commits: 7,806
Total Committers: 106
Avg Commits per committer: 73.642
Development Distribution Score (DDS): 0.417

Past Year

Commits: 3
Committers: 2
Avg Commits per committer: 1.5
Development Distribution Score (DDS): 0.333

Top Committers

Name	Email	Commits
chapmanb	c**b@5**m	4,548
roryk	r**r@g**m	1,436
Lorena Pantano	l**o@g**m	430
Sergey Naumenko	n****a	386
Matthias De Smet	m**t@u**e	101
Luca Beltrame	l**e@m**t	86
Ilya Sytchev	i**v@h**u	80
Tetiana Khotiaintseva	t**a@a**m	79
klrl262	m**i@a**m	57
Roman Valls Guimera	r**a@s**e	54
vladsaveliev	v**v@m**m	54
Roman Valls Guimera	b**m@n**g	41
vladsaveliev	v**v@g**m	35
Christian Brueffer	c**n@b**e	34
John Kern	k**0@g**m	31
naumenko.sa	e**b@g**m	29
Guillermo Carrasco	g**8@g**m	24
Miika Ahdesmaki	m**i@l**i	16
Ahdesmaki, Miika J	M**i@a**m	16
Paul Tang	t**g@g**m	16
Tetiana Khotiaintseva	t**t@g**m	14
James Porter	p**j@g**m	12
Sehrish Kanwal	k**s@u**u	12
Roman Valls Guimerà	r**g@k**e	10
biocyberman	b**n@g**m	10
Alexandru Coman	a**n@c**m	8
bogdang989	b**c@s**m	7
Roman Valls Guimera	r**n@l**m	7
Mario Giovacchini	m**o@s**e	7
Mario Giovacchini	m**i@s**e	7
and 76 more...

Committer Domains (Top 20 + Academic)

astrazeneca.com: 4 scilifelab.se: 4 limbus-medtec.com: 3 tgen.org: 2 curoverse.com: 2 unimelb.edu.au: 2 ucsf.edu: 2 ovi.com: 1 gmx.de: 1 nxn.se: 1 debian.org: 1 lifesum.com: 1 sbgenomics.com: 1 cloudbasesolutions.com: 1 kth.se: 1 live.fi: 1 brueffer.de: 1 nopcode.org: 1 me.com: 1 ardigen.com: 1 hsph.harvard.edu: 1 fas.harvard.edu: 1 imp.ac.at: 1 ebi.ac.uk: 1 hms.harvard.edu: 1 asu.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 127
Total pull requests: 21
Average time to close issues: 2 months
Average time to close pull requests: 4 months
Total issue authors: 78
Total pull request authors: 12
Average comments per issue: 3.95
Average comments per pull request: 1.1
Merged pull requests: 14
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 0
Average time to close issues: 7 minutes
Average time to close pull requests: N/A
Issue authors: 2
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

gis-nlsim (11)
amizeranschi (10)
rchekaluk (5)
prasundutta87 (4)
mjsduncan (4)
DiyaVaka (3)
lovebaboon1989 (3)
wangpenhok (3)
hanaecarrie (2)
keenhl (2)
tpham2654 (2)
Talo07 (2)
Adrian-Zet (2)
gabeng (2)
fardellas (2)

Pull Request Authors

naumenko-sa (8)
lbeltrame (3)
matthdsm (2)
a-detiste (2)
mistrm82 (1)
amizeranschi (1)
timgates42 (1)
asee-imagia (1)
rchekaluk (1)
lpantano (1)
TrellixVulnTeam (1)
Gammerdinger (1)

Top Labels

Issue Labels

bug (2) question (2) enhancement (1)

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- pypi 166 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 15
(may contain duplicates)
Total versions: 122
Total maintainers: 1

pypi.org: bcbio-nextgen

Best-practice pipelines for fully automated high throughput sequencing analysis

Homepage: https://github.com/bcbio/bcbio-nextgen
Documentation: https://bcbio-nextgen.readthedocs.io/
License: MIT
Latest release: 1.1.5
published almost 7 years ago

Versions: 57
Dependent Packages: 0
Dependent Repositories: 15
Downloads: 166 Last month
Docker Downloads: 0

Rankings

Docker downloads count: 1.3%

Stargazers count: 2.1%

Forks count: 2.8%

Dependent repos count: 3.7%

Average: 5.7%

Dependent packages count: 10.1%

Downloads: 14.2%

Maintainers (1)

chapmanb

Last synced: 7 months ago

proxy.golang.org: github.com/bcbio/bcbio-nextgen

Documentation: https://pkg.go.dev/github.com/bcbio/bcbio-nextgen#section-documentation
License: mit
Latest release: v1.2.9
published over 4 years ago

Versions: 65
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 7.0%

Average: 8.2%

Dependent repos count: 9.3%

Last synced: 7 months ago

Dependencies

docs/requirements-local.txt pypi

sphinx ==2.1.2
sphinx_rtd_theme ==0.4.3

docs/requirements.txt pypi

myst-parser ==0.14.0

requirements-conda.txt pypi

bcbio-nextgen =1.2.9

requirements-dev.txt pypi

flake8 *
pytest *

requirements.txt pypi

bcbio-nextgen ==1.2.9

setup.py pypi

bcbio-nextgen

Science Score: 46.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

Features

Quick start

Documentation

Contributors

License

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: bcbio-nextgen

Rankings

Maintainers (1)

proxy.golang.org: github.com/bcbio/bcbio-nextgen

Rankings

Dependencies