René's URL Explorer Experiment


Title: GitHub - bactopia/bactopia: A flexible pipeline for complete analysis of bacterial genomes · GitHub

Open Graph Title: GitHub - bactopia/bactopia: A flexible pipeline for complete analysis of bacterial genomes

X Title: GitHub - bactopia/bactopia: A flexible pipeline for complete analysis of bacterial genomes

Description: A flexible pipeline for complete analysis of bacterial genomes - bactopia/bactopia

Open Graph Description: A flexible pipeline for complete analysis of bacterial genomes - bactopia/bactopia

X Description: A flexible pipeline for complete analysis of bacterial genomes - bactopia/bactopia

Opengraph URL: https://github.com/bactopia/bactopia

X: @github

direct link

Domain: github.com

route-pattern/:user_id/:repository
route-controllerfiles
route-actiondisambiguate
fetch-noncev2:786f6ad7-6445-ffd6-fb54-a5a9ec78fae9
current-catalog-service-hashf3abb0cc802f3d7b95fc8762b94bdcb13bf39634c40c357301c4aa1d67a256fb
request-idCB68:3C5CB:E9CA78:144BE99:6A4E8C8D
html-safe-noncee880a1b61e6d1cfbe34915580ca8eac3cf7adaf67dd99c146aed695136f0eb28
visitor-payloadeyJyZWZlcnJlciI6IiIsInJlcXVlc3RfaWQiOiJDQjY4OjNDNUNCOkU5Q0E3ODoxNDRCRTk5OjZBNEU4QzhEIiwidmlzaXRvcl9pZCI6IjI2NTg0MTE5MTEzNDM2NzI0NjEiLCJyZWdpb25fZWRnZSI6ImlhZCIsInJlZ2lvbl9yZW5kZXIiOiJpYWQifQ==
visitor-hmac9568c0ebf59034ae09ff1f8becfeebe664d77a7061547469b039b73f255050a4
hovercard-subject-tagrepository:172074074
github-keyboard-shortcutsrepository,copilot
google-site-verificationApib7-x98H0j5cPqHWwSMm6dNU4GmODRoqxLiDzdx9I
octolytics-urlhttps://collector.github.com/github/collect
analytics-location//
fb:app_id1401488693436528
apple-itunes-appapp-id=1477376905, app-argument=https://github.com/bactopia/bactopia
twitter:imagehttps://repository-images.githubusercontent.com/172074074/8eab4d51-701f-48d9-9821-7dbc51e80657
twitter:cardsummary_large_image
og:imagehttps://repository-images.githubusercontent.com/172074074/8eab4d51-701f-48d9-9821-7dbc51e80657
og:image:altA flexible pipeline for complete analysis of bacterial genomes - bactopia/bactopia
og:site_nameGitHub
og:typeobject
hostnamegithub.com
expected-hostnamegithub.com
None41b6ab3ba6d20a71766ac245b5a4a94c6fc672a9cd4da7d44c1b33ab8bf6a21c
turbo-cache-controlno-cache
go-importgithub.com/bactopia/bactopia git https://github.com/bactopia/bactopia.git
octolytics-dimension-user_id49879847
octolytics-dimension-user_loginbactopia
octolytics-dimension-repository_id172074074
octolytics-dimension-repository_nwobactopia/bactopia
octolytics-dimension-repository_publictrue
octolytics-dimension-repository_is_forkfalse
octolytics-dimension-repository_network_root_id172074074
octolytics-dimension-repository_network_root_nwobactopia/bactopia
turbo-body-classeslogged-out env-production page-responsive
disable-turbofalse
browser-stats-urlhttps://api.github.com/_private/browser/stats
browser-errors-urlhttps://api.github.com/_private/browser/errors
releasee6a744804e8e70f97b4d5a18a94dcc63db22f97a
ui-targetfull
theme-color#1e2327
color-schemelight dark

Links:

Skip to contenthttps://github.com/bactopia/bactopia#start-of-content
https://github.com/
Sign in https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fbactopia%2Fbactopia
GitHub CopilotWrite better code with AIhttps://github.com/features/copilot
GitHub Copilot appDirect agents from issue to mergehttps://github.com/features/ai/github-app
MCP RegistryNewIntegrate external toolshttps://github.com/mcp
ActionsAutomate any workflowhttps://github.com/features/actions
CodespacesInstant dev environmentshttps://github.com/features/codespaces
IssuesPlan and track workhttps://github.com/features/issues
Code ReviewManage code changeshttps://github.com/features/code-review
GitHub Advanced SecurityFind and fix vulnerabilitieshttps://github.com/security/advanced-security
Code securitySecure your code as you buildhttps://github.com/security/advanced-security/code-security
Secret protectionStop leaks before they starthttps://github.com/security/advanced-security/secret-protection
Why GitHubhttps://github.com/why-github
Documentationhttps://docs.github.com
Bloghttps://github.blog
Changeloghttps://github.blog/changelog
Marketplacehttps://github.com/marketplace
View all featureshttps://github.com/features
Enterpriseshttps://github.com/enterprise
Small and medium teamshttps://github.com/team
Startupshttps://github.com/enterprise/startups
Nonprofitshttps://github.com/solutions/industry/nonprofits
App Modernizationhttps://github.com/solutions/use-case/app-modernization
DevSecOpshttps://github.com/solutions/use-case/devsecops
DevOpshttps://github.com/solutions/use-case/devops
CI/CDhttps://github.com/solutions/use-case/ci-cd
View all use caseshttps://github.com/solutions/use-case
Healthcarehttps://github.com/solutions/industry/healthcare
Financial serviceshttps://github.com/solutions/industry/financial-services
Manufacturinghttps://github.com/solutions/industry/manufacturing
Governmenthttps://github.com/solutions/industry/government
View all industrieshttps://github.com/solutions/industry
View all solutionshttps://github.com/solutions
AIhttps://github.com/resources/articles?topic=ai
Software Developmenthttps://github.com/resources/articles?topic=software-development
DevOpshttps://github.com/resources/articles?topic=devops
Securityhttps://github.com/resources/articles?topic=security
View all topicshttps://github.com/resources/articles
Customer storieshttps://github.com/customer-stories
Events & webinarshttps://github.com/resources/events
Ebooks & reportshttps://github.com/resources/whitepapers
Business insightshttps://github.com/solutions/executive-insights
GitHub Skillshttps://skills.github.com
Documentationhttps://docs.github.com
Customer supporthttps://support.github.com
Community forumhttps://github.com/orgs/community/discussions
Trust centerhttps://github.com/trust-center
Partnershttps://github.com/partners
View all resourceshttps://github.com/resources
GitHub SponsorsFund open source developershttps://github.com/open-source/sponsors
Security Labhttps://securitylab.github.com
Maintainer Communityhttps://maintainers.github.com
Acceleratorhttps://github.com/open-source/accelerator
GitHub Starshttps://stars.github.com
Archive Programhttps://archiveprogram.github.com
Topicshttps://github.com/topics
Trendinghttps://github.com/trending
Collectionshttps://github.com/collections
Enterprise platformAI-powered developer platformhttps://github.com/enterprise
GitHub Advanced SecurityEnterprise-grade security featureshttps://github.com/security/advanced-security
Copilot for BusinessEnterprise-grade AI featureshttps://github.com/features/copilot/copilot-business
Premium SupportEnterprise-grade 24/7 supporthttps://github.com/enterprise/premium-support
Pricinghttps://github.com/pricing
Search syntax tipshttps://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
documentationhttps://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
Sign in https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fbactopia%2Fbactopia
Sign up https://github.com/signup?ref_cta=Sign+up&ref_loc=header+logged+out&ref_page=%2F%3Cuser-name%3E%2F%3Crepo-name%3E&source=header-repo&source_repo=bactopia%2Fbactopia
Reloadhttps://github.com/bactopia/bactopia
Reloadhttps://github.com/bactopia/bactopia
Reloadhttps://github.com/bactopia/bactopia
Please reload this pagehttps://github.com/bactopia/bactopia
bactopia https://github.com/bactopia
bactopiahttps://github.com/bactopia/bactopia
Notifications https://github.com/login?return_to=%2Fbactopia%2Fbactopia
Fork 80 https://github.com/login?return_to=%2Fbactopia%2Fbactopia
Star 517 https://github.com/login?return_to=%2Fbactopia%2Fbactopia
Code https://github.com/bactopia/bactopia
Issues 75 https://github.com/bactopia/bactopia/issues
Pull requests 2 https://github.com/bactopia/bactopia/pulls
Actions https://github.com/bactopia/bactopia/actions
Projects https://github.com/bactopia/bactopia/projects
Security and quality 0 https://github.com/bactopia/bactopia/security
Insights https://github.com/bactopia/bactopia/pulse
Code https://github.com/bactopia/bactopia
Issues https://github.com/bactopia/bactopia/issues
Pull requests https://github.com/bactopia/bactopia/pulls
Actions https://github.com/bactopia/bactopia/actions
Projects https://github.com/bactopia/bactopia/projects
Security and quality https://github.com/bactopia/bactopia/security
Insights https://github.com/bactopia/bactopia/pulse
https://github.com/bactopia/bactopia
Brancheshttps://github.com/bactopia/bactopia/branches
Tagshttps://github.com/bactopia/bactopia/tags
https://github.com/bactopia/bactopia/branches
https://github.com/bactopia/bactopia/tags
1,633 Commitshttps://github.com/bactopia/bactopia/commits/master/
https://github.com/bactopia/bactopia/commits/master/
.claudehttps://github.com/bactopia/bactopia/tree/master/.claude
.claudehttps://github.com/bactopia/bactopia/tree/master/.claude
.githubhttps://github.com/bactopia/bactopia/tree/master/.github
.githubhttps://github.com/bactopia/bactopia/tree/master/.github
.vscodehttps://github.com/bactopia/bactopia/tree/master/.vscode
.vscodehttps://github.com/bactopia/bactopia/tree/master/.vscode
binhttps://github.com/bactopia/bactopia/tree/master/bin
binhttps://github.com/bactopia/bactopia/tree/master/bin
confhttps://github.com/bactopia/bactopia/tree/master/conf
confhttps://github.com/bactopia/bactopia/tree/master/conf
datahttps://github.com/bactopia/bactopia/tree/master/data
datahttps://github.com/bactopia/bactopia/tree/master/data
moduleshttps://github.com/bactopia/bactopia/tree/master/modules
moduleshttps://github.com/bactopia/bactopia/tree/master/modules
subworkflowshttps://github.com/bactopia/bactopia/tree/master/subworkflows
subworkflowshttps://github.com/bactopia/bactopia/tree/master/subworkflows
testshttps://github.com/bactopia/bactopia/tree/master/tests
testshttps://github.com/bactopia/bactopia/tree/master/tests
workflowshttps://github.com/bactopia/bactopia/tree/master/workflows
workflowshttps://github.com/bactopia/bactopia/tree/master/workflows
.gitignorehttps://github.com/bactopia/bactopia/blob/master/.gitignore
.gitignorehttps://github.com/bactopia/bactopia/blob/master/.gitignore
CHANGELOG.mdhttps://github.com/bactopia/bactopia/blob/master/CHANGELOG.md
CHANGELOG.mdhttps://github.com/bactopia/bactopia/blob/master/CHANGELOG.md
CITATION.cffhttps://github.com/bactopia/bactopia/blob/master/CITATION.cff
CITATION.cffhttps://github.com/bactopia/bactopia/blob/master/CITATION.cff
CLAUDE.mdhttps://github.com/bactopia/bactopia/blob/master/CLAUDE.md
CLAUDE.mdhttps://github.com/bactopia/bactopia/blob/master/CLAUDE.md
CODE_OF_CONDUCT.mdhttps://github.com/bactopia/bactopia/blob/master/CODE_OF_CONDUCT.md
CODE_OF_CONDUCT.mdhttps://github.com/bactopia/bactopia/blob/master/CODE_OF_CONDUCT.md
CONTRIBUTING.mdhttps://github.com/bactopia/bactopia/blob/master/CONTRIBUTING.md
CONTRIBUTING.mdhttps://github.com/bactopia/bactopia/blob/master/CONTRIBUTING.md
LICENSEhttps://github.com/bactopia/bactopia/blob/master/LICENSE
LICENSEhttps://github.com/bactopia/bactopia/blob/master/LICENSE
README.mdhttps://github.com/bactopia/bactopia/blob/master/README.md
README.mdhttps://github.com/bactopia/bactopia/blob/master/README.md
catalog.jsonhttps://github.com/bactopia/bactopia/blob/master/catalog.json
catalog.jsonhttps://github.com/bactopia/bactopia/blob/master/catalog.json
environment.ymlhttps://github.com/bactopia/bactopia/blob/master/environment.yml
environment.ymlhttps://github.com/bactopia/bactopia/blob/master/environment.yml
llms.txthttps://github.com/bactopia/bactopia/blob/master/llms.txt
llms.txthttps://github.com/bactopia/bactopia/blob/master/llms.txt
main.nfhttps://github.com/bactopia/bactopia/blob/master/main.nf
main.nfhttps://github.com/bactopia/bactopia/blob/master/main.nf
nextflow.confighttps://github.com/bactopia/bactopia/blob/master/nextflow.config
nextflow.confighttps://github.com/bactopia/bactopia/blob/master/nextflow.config
nextflow_schema.jsonhttps://github.com/bactopia/bactopia/blob/master/nextflow_schema.json
nextflow_schema.jsonhttps://github.com/bactopia/bactopia/blob/master/nextflow_schema.json
READMEhttps://github.com/bactopia/bactopia
Code of conducthttps://github.com/bactopia/bactopia
Contributinghttps://github.com/bactopia/bactopia
MIT licensehttps://github.com/bactopia/bactopia
https://github.com/bactopia/bactopia/releases
https://doi.org/10.1128/mSystems.00190-20
https://anaconda.org/bioconda/bactopia
https://github.com/bactopia/bactopia/blob/master/data/bactopia-logo.png
https://github.com/bactopia/bactopia#bactopia
Bactopia Analysis Pipelinehttps://bactopia.io/beginners-guide/
Bactopia Toolshttps://bactopia.io/bactopia-tools/
Nextflowhttps://www.nextflow.io/
https://github.com/bactopia/bactopia/blob/master/data/bactopia-workflow.png
predictable output structurehttps://bactopia.io/full-guide/
Staphopiahttps://staphopia.github.io/
https://github.com/bactopia/bactopia#documentation
https://bactopia.io/https://bactopia.io/
Staphopiahttps://staphopia.github.io/
https://github.com/bactopia/bactopia#quick-start
https://github.com/bactopia/bactopia#installation
Condahttps://conda.io/en/latest/
official Conda documentationhttps://conda.io/projects/conda/en/latest/user-guide/install/index.html
Miniforge installerhttps://github.com/conda-forge/miniforgel
Anaconda installerhttps://www.anaconda.com/distribution/
https://github.com/bactopia/bactopia#please-cite-datasets-and-tools
A list of each dataset/tool used by Bactopia has been made availablehttps://bactopia.io/impact-and-outreach/acknowledgements/
https://github.com/bactopia/bactopia#acknowledgements
https://github.com/bactopia/bactopia#alternatives
reach outhttps://github.com/bactopia/bactopia/issues/new/choose
AQUAMIShttps://gitlab.com/bfr_bioinformatics/AQUAMIS
ASA³Phttps://github.com/oschwengers/asap
https://doi.org/10.1371/journal.pcbi.1007134https://doi.org/10.1371/journal.pcbi.1007134
MicroPIPEhttps://github.com/BeatsonLab-MicrobialGenomics/micropipe
https://doi.org/10.1186/s12864-021-07767-zhttps://doi.org/10.1186/s12864-021-07767-z
Nullarborhttps://github.com/tseemann/nullarbor
https://github.com/tseemann/nullarborhttps://github.com/tseemann/nullarbor
ProkEvohttps://github.com/npavlovikj/ProkEvo
https://doi.org/10.7717/peerj.11376https://doi.org/10.7717/peerj.11376
Public Health Bacterial Genomicshttps://github.com/theiagen/public_health_bacterial_genomics
https://github.com/theiagen/public_health_bacterial_genomicshttps://github.com/theiagen/public_health_bacterial_genomics
rMAPhttps://github.com/GunzIvan28/rMAP
https://doi.org/10.1099/mgen.0.000583https://doi.org/10.1099/mgen.0.000583
TORMEShttps://github.com/nmquijada/tormes
https://doi.org/10.1093/bioinformatics/btz220https://doi.org/10.1093/bioinformatics/btz220
https://github.com/bactopia/bactopia#feedback
Issue Trackerhttps://github.com/bactopia/bactopia/issues
https://github.com/bactopia/bactopia#license
MIT Licensehttps://raw.githubusercontent.com/bactopia/bactopia/master/LICENSE
https://github.com/bactopia/bactopia#citation
https://doi.org/10.1128/mSystems.00190-20https://doi.org/10.1128/mSystems.00190-20
https://github.com/bactopia/bactopia#author
@rpetit3https://bsky.app/profile/rpetit3.bsky.social
https://github.com/bactopia/bactopia#funding
CDC Emerging Infections Program (U50CK000485) PPHF/ACA: Enhancing Epidemiology and Laboratory Capacityhttps://dph.georgia.gov/EIP
Wyoming Public Health Divisionhttps://health.wyo.gov/publichealth/
Center for Applied Pathogen Epidemiology and Outbreak Control (CAPE)https://www.linkedin.com/company/center-for-applied-pathogen-epidemiology-and-outbreak-control/
CZI Open Science Program (EOSS6)https://chanzuckerberg.com/eoss/proposals/enhancing-the-bactopia-ecosystem-with-trainings-and-visual-reports/
https://github.com/bactopia/bactopia/blob/master/data/gaeip-banner.png
https://github.com/bactopia/bactopia/blob/master/data/wyphd-banner.jpg
https://github.com/bactopia/bactopia/blob/master/data/cape-banner.png
https://github.com/bactopia/bactopia/blob/master/data/czi-banner.png
bactopia.iohttps://bactopia.io
nextflow https://github.com/topics/nextflow
conda https://github.com/topics/conda
bioconda https://github.com/topics/bioconda
bacterial-genomes https://github.com/topics/bacterial-genomes
fastqs https://github.com/topics/fastqs
Readme https://github.com/bactopia/bactopia#readme-ov-file
MIT license https://github.com/bactopia/bactopia#MIT-1-ov-file
Code of conduct https://github.com/bactopia/bactopia#coc-ov-file
Contributing https://github.com/bactopia/bactopia#contributing-ov-file
Please reload this pagehttps://github.com/bactopia/bactopia
Activityhttps://github.com/bactopia/bactopia/activity
Custom propertieshttps://github.com/bactopia/bactopia/custom-properties
80 forkshttps://github.com/bactopia/bactopia/forks
Report repository https://github.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2Fbactopia%2Fbactopia&report=bactopia+%28user%29
Releases 52https://github.com/bactopia/bactopia/releases
v4.0.0 Latest Apr 29, 2026 https://github.com/bactopia/bactopia/releases/tag/v4.0.0
+ 51 releaseshttps://github.com/bactopia/bactopia/releases
Packages 0https://github.com/orgs/bactopia/packages?repo_name=bactopia
Please reload this pagehttps://github.com/bactopia/bactopia
Please reload this pagehttps://github.com/bactopia/bactopia
Contributorshttps://github.com/bactopia/bactopia/graphs/contributors
Please reload this pagehttps://github.com/bactopia/bactopia
Nextflow 92.9% https://github.com/bactopia/bactopia/search?l=nextflow
Perl 4.8% https://github.com/bactopia/bactopia/search?l=perl
Shell 2.0% https://github.com/bactopia/bactopia/search?l=shell
Python 0.3% https://github.com/bactopia/bactopia/search?l=python
https://github.com
Termshttps://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacyhttps://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Securityhttps://github.com/security
Statushttps://www.githubstatus.com/
Communityhttps://github.community/
Docshttps://docs.github.com/
Contacthttps://support.github.com?tags=dotcom-footer

Viewport: width=device-width


URLs of crawlers that visited me.