metagenome-atlas

ATLAS - Three commands to start analyzing your metagenome data

https://github.com/metagenome-atlas/atlas

Science Score: 49.0%

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

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
✓
Committers with academic emails
6 of 37 committers (16.2%) 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 (10.1%) to scientific vocabulary

Keywords

annotation assembly functional-annotation genomic-binning metagenomics snakemake taxonomic-classifications

Keywords from Contributors

bioinformatics microbiome sequences metabarcoding nextflow networks workflows interpretability standardization animal

Last synced: 6 months ago · JSON representation

Repository

ATLAS - Three commands to start analyzing your metagenome data

Basic Info

Host: GitHub
Owner: metagenome-atlas
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://metagenome-atlas.github.io/
Size: 20.3 MB

Statistics

Stars: 390
Watchers: 14
Forks: 100
Open Issues: 15
Releases: 59

Topics

annotation assembly functional-annotation genomic-binning metagenomics snakemake taxonomic-classifications

Created about 9 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog Contributing License

Metagenome-Atlas

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.

scheme of workflow

You can start using atlas with three commands:

sh mamba install -y -c bioconda -c conda-forge metagenome-atlas={latest_version} atlas init --db-dir databases path/to/fastq/files atlas run all

where {latest_version} should be replaced by

Webpage

metagenome-atlas.github.io

Documentation

https://metagenome-atlas.readthedocs.io/

Tutorial

Citation

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.
Kieser, S., Brown, J., Zdobnov, E. M., Trajkovski, M. & McCue, L. A. BMC Bioinformatics 21, 257 (2020).
doi: 10.1186/s12859-020-03585-4

Development/Extensions

Here are some ideas I work or want to work on when I have time. If you want to contribute or have some ideas let me know via a feature request issue.

Optimized MAG recovery (e.g. Spacegraphcats)
Integration of viruses/plasmid that live for now as extensions
Add statistics and visualisations as in atlas_analyze
Implementation of most rules as snakemake wrapper
Cloud execution
Update to new Snakemake version and use cool reports.

Owner

Name: metagenome-atlas
Login: metagenome-atlas
Kind: organization

Repositories: 27
Profile: https://github.com/metagenome-atlas

GitHub Events

Total

Issues event: 39
Watch event: 21
Delete event: 1
Issue comment event: 51
Push event: 10
Pull request review event: 1
Pull request event: 3
Fork event: 3
Create event: 5

Last Year

Issues event: 39
Watch event: 21
Delete event: 1
Issue comment event: 51
Push event: 10
Pull request review event: 1
Pull request event: 3
Fork event: 3
Create event: 5

Committers

Last synced: 9 months ago

All Time

Total Commits: 2,455
Total Committers: 37
Avg Commits per committer: 66.351
Development Distribution Score (DDS): 0.247

Past Year

Commits: 36
Committers: 3
Avg Commits per committer: 12.0
Development Distribution Score (DDS): 0.083

Top Committers

Name	Email	Commits
kiesers	s**r@g**m	1,849
Joe Brown	j**n@p**v	337
Joe Brown	b**m@g**m	75
“Sean	“**y@g**”	45
Sean Colby	s**y@g**m	44
Richard Allen White III	r**7@g**m	37
yanhui09	me@y****g	8
Brown, Joe	j**n@p**v	6
Jackson Tsuji	j**i@u**a	6
Jackson M. Tsuji	j**i@u**a	4
Silvio Waschina	3****a	4
Cedric Midoux	c**x@i**r	4
John Sundh	j**h@s**e	4
Mladen Rasic	m****0	4
Chris Overall	n**o@g**m	2
Johannes Zimmermann	jo@j****t	2
Mattias	m**r@n**l	2
Silas Kieser	s**r@g**m	2
Silas Kieser	s**s@S**l	2
Aron Arzoomand	5****z	1
C. Titus Brown	t**s@i**g	1
Christopher Bottoms	m****s	1
Colin Brislawn	c**l@g**m	1
silas kieser	r**1@g**m	1
Yan Hui	y**i@g**r	1
Silas Kieser	k**r@b**h	1
Sean M Colby	c**4@c**v	1
Richard A White	w**0@c**v	1
KIESER Silas	k**s@l**b	1
LLansing	3****g	1
and 7 more...

Committer Domains (Top 20 + Academic)

pnnl.gov: 2 uwaterloo.ca: 2 gmail.com”: 1 yanh.org: 1 inrae.fr: 1 scilifelab.se: 1 jotech.net: 1 nioo.knaw.nl: 1 gmiail.com: 1 idyll.org: 1 gate.nihs.ch.nestle.com: 1 g-12-l0002.cm.cluster: 1 bee.unige.ch: 1 constance01.pnl.gov: 1 constance03.pnl.gov: 1 login2.baobab: 1 a3.epfl.ch: 1 roshnibiswas.tech: 1 126.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 135
Total pull requests: 60
Average time to close issues: 8 months
Average time to close pull requests: about 2 months
Total issue authors: 80
Total pull request authors: 14
Average comments per issue: 4.41
Average comments per pull request: 0.63
Merged pull requests: 42
Bot issues: 0
Bot pull requests: 2

Past Year

Issues: 20
Pull requests: 3
Average time to close issues: about 2 months
Average time to close pull requests: 2 days
Issue authors: 11
Pull request authors: 2
Average comments per issue: 1.85
Average comments per pull request: 1.33
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

SilasK (15)
mladen5000 (8)
jotech (8)
bioinfogini (6)
Sofie8 (3)
luozhy88 (3)
trickovicmatija (2)
JustinGibbons (2)
bcpd (2)
ShevchenkoAlla (2)
rjain1990 (2)
dingxm (2)
the-eon-flux (2)
IRSADFERHAT (2)
almutwerner (2)

Pull Request Authors

SilasK (45)
johnne (3)
github-actions[bot] (3)
mladen5000 (3)
CedricMidoux (2)
njohner (2)
Waschina (2)
mortonjt (2)
philippbayer (1)
trickovicmatija (1)
strejcem (1)
AroArz (1)
LLansing (1)
jotech (1)

Top Labels

Issue Labels

stale (58) Feature request (16) enhancement (1) minor bug (1) Known issue (1) bug (1) autorelease: pending (1) keep (1)

Pull Request Labels

autorelease: pending (2) stale (1) autorelease: tagged (1)

Packages

Total packages: 1
Total downloads:
- pypi 17 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 2
Total maintainers: 2

pypi.org: metagenome-atlas

ATLAS - workflows for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data.

Homepage: https://github.com/metagenome-atlas/atlas
Documentation: https://metagenome-atlas.readthedocs.io/
License: BSD-3
Latest release: 2.0.0
published about 7 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 17 Last month

Rankings

Stargazers count: 3.5%

Forks count: 4.7%

Dependent packages count: 10.1%

Average: 18.9%

Dependent repos count: 21.5%

Downloads: 54.7%

Maintainers (2)

brwnj silask

Last synced: 6 months ago

Dependencies

.github/workflows/python-package-conda.yml actions

actions/cache v2 composite
actions/checkout v3.5.2 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/stale.yml actions

actions/stale v7 composite

metagenome-atlas

Science Score: 49.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Metagenome-Atlas

Webpage

Documentation

Citation

Development/Extensions

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: metagenome-atlas

Rankings

Maintainers (2)

Dependencies