René's URL Explorer Experiment


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

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: patch-diff.githubusercontent.com

route-pattern/:user_id/:repository
route-controllerfiles
route-actiondisambiguate
fetch-noncev2:e88b501f-8d63-4c07-ecfd-2207f940ddb9
current-catalog-service-hashf3abb0cc802f3d7b95fc8762b94bdcb13bf39634c40c357301c4aa1d67a256fb
request-idA68A:1D9B97:7F55564:A3C0DFE:6975B91E
html-safe-noncea0baa77014f805029f975ec7797e1c65fb45a5a7042fabaddbc3e95e851f9d04
visitor-payloadeyJyZWZlcnJlciI6IiIsInJlcXVlc3RfaWQiOiJBNjhBOjFEOUI5Nzo3RjU1NTY0OkEzQzBERkU6Njk3NUI5MUUiLCJ2aXNpdG9yX2lkIjoiODU2ODgwNjI5NjcyNTYwMDU0MiIsInJlZ2lvbl9lZGdlIjoiaWFkIiwicmVnaW9uX3JlbmRlciI6ImlhZCJ9
visitor-hmac60673e5907a291f71bccc0cd5c52bdf964a72b1d14fa4b5279ec798c411f5219
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
None4a4bf5f4e28041a9d2e5c107d7d20b78b4294ba261cab243b28167c16a623a1f
turbo-cache-controlno-preview
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
release488b30e96dfd057fbbe44c6665ccbc030b729dde
ui-targetfull
theme-color#1e2327
color-schemelight dark

Links:

Skip to contenthttps://patch-diff.githubusercontent.com/bactopia/bactopia#start-of-content
https://patch-diff.githubusercontent.com/
Sign in https://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2Fbactopia%2Fbactopia
GitHub CopilotWrite better code with AIhttps://github.com/features/copilot
GitHub SparkBuild and deploy intelligent appshttps://github.com/features/spark
GitHub ModelsManage and compare promptshttps://github.com/features/models
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
GitHub SponsorsFund open source developershttps://github.com/sponsors
Security Labhttps://securitylab.github.com
Maintainer Communityhttps://maintainers.github.com
Acceleratorhttps://github.com/accelerator
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/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://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2Fbactopia%2Fbactopia
Sign up https://patch-diff.githubusercontent.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://patch-diff.githubusercontent.com/bactopia/bactopia
Reloadhttps://patch-diff.githubusercontent.com/bactopia/bactopia
Reloadhttps://patch-diff.githubusercontent.com/bactopia/bactopia
bactopia https://patch-diff.githubusercontent.com/bactopia
bactopiahttps://patch-diff.githubusercontent.com/bactopia/bactopia
Notifications https://patch-diff.githubusercontent.com/login?return_to=%2Fbactopia%2Fbactopia
Fork 79 https://patch-diff.githubusercontent.com/login?return_to=%2Fbactopia%2Fbactopia
Star 496 https://patch-diff.githubusercontent.com/login?return_to=%2Fbactopia%2Fbactopia
bactopia.github.iohttps://bactopia.github.io
MIT license https://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/LICENSE
496 stars https://patch-diff.githubusercontent.com/bactopia/bactopia/stargazers
79 forks https://patch-diff.githubusercontent.com/bactopia/bactopia/forks
Branches https://patch-diff.githubusercontent.com/bactopia/bactopia/branches
Tags https://patch-diff.githubusercontent.com/bactopia/bactopia/tags
Activity https://patch-diff.githubusercontent.com/bactopia/bactopia/activity
Star https://patch-diff.githubusercontent.com/login?return_to=%2Fbactopia%2Fbactopia
Notifications https://patch-diff.githubusercontent.com/login?return_to=%2Fbactopia%2Fbactopia
Code https://patch-diff.githubusercontent.com/bactopia/bactopia
Issues 101 https://patch-diff.githubusercontent.com/bactopia/bactopia/issues
Pull requests 1 https://patch-diff.githubusercontent.com/bactopia/bactopia/pulls
Actions https://patch-diff.githubusercontent.com/bactopia/bactopia/actions
Projects 0 https://patch-diff.githubusercontent.com/bactopia/bactopia/projects
Security 0 https://patch-diff.githubusercontent.com/bactopia/bactopia/security
Insights https://patch-diff.githubusercontent.com/bactopia/bactopia/pulse
Code https://patch-diff.githubusercontent.com/bactopia/bactopia
Issues https://patch-diff.githubusercontent.com/bactopia/bactopia/issues
Pull requests https://patch-diff.githubusercontent.com/bactopia/bactopia/pulls
Actions https://patch-diff.githubusercontent.com/bactopia/bactopia/actions
Projects https://patch-diff.githubusercontent.com/bactopia/bactopia/projects
Security https://patch-diff.githubusercontent.com/bactopia/bactopia/security
Insights https://patch-diff.githubusercontent.com/bactopia/bactopia/pulse
Brancheshttps://patch-diff.githubusercontent.com/bactopia/bactopia/branches
Tagshttps://patch-diff.githubusercontent.com/bactopia/bactopia/tags
https://patch-diff.githubusercontent.com/bactopia/bactopia/branches
https://patch-diff.githubusercontent.com/bactopia/bactopia/tags
1,632 Commitshttps://patch-diff.githubusercontent.com/bactopia/bactopia/commits/master/
https://patch-diff.githubusercontent.com/bactopia/bactopia/commits/master/
.githubhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/.github
.githubhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/.github
.skeletonhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/.skeleton
.skeletonhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/.skeleton
.vscodehttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/.vscode
.vscodehttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/.vscode
binhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/bin
binhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/bin
confhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/conf
confhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/conf
datahttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/data
datahttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/data
libhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/lib
libhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/lib
moduleshttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/modules
moduleshttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/modules
subworkflows/localhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/subworkflows/local
subworkflows/localhttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/subworkflows/local
testshttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/tests
testshttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/tests
workflowshttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/workflows
workflowshttps://patch-diff.githubusercontent.com/bactopia/bactopia/tree/master/workflows
.gitignorehttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/.gitignore
.gitignorehttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/.gitignore
.gitpod.ymlhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/.gitpod.yml
.gitpod.ymlhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/.gitpod.yml
CHANGELOG.mdhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/CHANGELOG.md
CHANGELOG.mdhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/CHANGELOG.md
CITATION.cffhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/CITATION.cff
CITATION.cffhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/CITATION.cff
CODE_OF_CONDUCT.mdhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/CODE_OF_CONDUCT.md
CODE_OF_CONDUCT.mdhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/CODE_OF_CONDUCT.md
CONTRIBUTING.mdhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/CONTRIBUTING.md
CONTRIBUTING.mdhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/CONTRIBUTING.md
LICENSEhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/LICENSE
LICENSEhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/LICENSE
README.mdhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/README.md
README.mdhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/README.md
citations.ymlhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/citations.yml
citations.ymlhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/citations.yml
main.nfhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/main.nf
main.nfhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/main.nf
nextflow.confighttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/nextflow.config
nextflow.confighttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/nextflow.config
nextflow_schema.jsonhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/nextflow_schema.json
nextflow_schema.jsonhttps://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/nextflow_schema.json
READMEhttps://patch-diff.githubusercontent.com/bactopia/bactopia
Code of conducthttps://patch-diff.githubusercontent.com/bactopia/bactopia
Contributinghttps://patch-diff.githubusercontent.com/bactopia/bactopia
MIT licensehttps://patch-diff.githubusercontent.com/bactopia/bactopia
https://github.com/bactopia/bactopia/releases
https://doi.org/10.1128/mSystems.00190-20
https://anaconda.org/bioconda/bactopia
https://gitpod.io/#https://github.com/bactopia/bactopia
https://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/data/bactopia-logo.png
https://patch-diff.githubusercontent.com/bactopia/bactopia#bactopia
Bactopia Analysis Pipelinehttps://bactopia.github.io/latest/beginners-guide/
Bactopia Toolshttps://bactopia.github.io/latest/bactopia-tools/
Nextflowhttps://www.nextflow.io/
https://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/data/bactopia-workflow.png
predictable output structurehttps://bactopia.github.io/latest/full-guide/
Staphopiahttps://staphopia.github.io/
https://patch-diff.githubusercontent.com/bactopia/bactopia#documentation
https://bactopia.github.io/https://bactopia.github.io/
Staphopiahttps://staphopia.github.io/
https://patch-diff.githubusercontent.com/bactopia/bactopia#quick-start
https://patch-diff.githubusercontent.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://patch-diff.githubusercontent.com/bactopia/bactopia#please-cite-datasets-and-tools
A list of each dataset/tool used by Bactopia has been made availablehttps://bactopia.github.io/latest/impact-and-outreach/acknowledgements/
https://patch-diff.githubusercontent.com/bactopia/bactopia#acknowledgements
https://patch-diff.githubusercontent.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://patch-diff.githubusercontent.com/bactopia/bactopia#feedback
Issue Trackerhttps://github.com/bactopia/bactopia/issues
https://patch-diff.githubusercontent.com/bactopia/bactopia#license
MIT Licensehttps://raw.githubusercontent.com/bactopia/bactopia/master/LICENSE
https://patch-diff.githubusercontent.com/bactopia/bactopia#citation
https://doi.org/10.1128/mSystems.00190-20https://doi.org/10.1128/mSystems.00190-20
https://patch-diff.githubusercontent.com/bactopia/bactopia#author
@rpetit3https://twitter.com/rpetit3
https://patch-diff.githubusercontent.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/
https://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/data/gaeip-banner.png
https://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/data/wyphd-banner.jpg
https://patch-diff.githubusercontent.com/bactopia/bactopia/blob/master/data/cape-banner.png
bactopia.github.iohttps://bactopia.github.io
nextflow https://patch-diff.githubusercontent.com/topics/nextflow
conda https://patch-diff.githubusercontent.com/topics/conda
bioconda https://patch-diff.githubusercontent.com/topics/bioconda
bacterial-genomes https://patch-diff.githubusercontent.com/topics/bacterial-genomes
fastqs https://patch-diff.githubusercontent.com/topics/fastqs
Readme https://patch-diff.githubusercontent.com/bactopia/bactopia#readme-ov-file
MIT license https://patch-diff.githubusercontent.com/bactopia/bactopia#MIT-1-ov-file
Code of conduct https://patch-diff.githubusercontent.com/bactopia/bactopia#coc-ov-file
Contributing https://patch-diff.githubusercontent.com/bactopia/bactopia#contributing-ov-file
Please reload this pagehttps://patch-diff.githubusercontent.com/bactopia/bactopia
Activityhttps://patch-diff.githubusercontent.com/bactopia/bactopia/activity
Custom propertieshttps://patch-diff.githubusercontent.com/bactopia/bactopia/custom-properties
496 starshttps://patch-diff.githubusercontent.com/bactopia/bactopia/stargazers
15 watchinghttps://patch-diff.githubusercontent.com/bactopia/bactopia/watchers
79 forkshttps://patch-diff.githubusercontent.com/bactopia/bactopia/forks
Report repository https://patch-diff.githubusercontent.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2Fbactopia%2Fbactopia&report=bactopia+%28user%29
Releases 51https://patch-diff.githubusercontent.com/bactopia/bactopia/releases
v3.2.0 Latest Mar 21, 2025 https://patch-diff.githubusercontent.com/bactopia/bactopia/releases/tag/v3.2.0
+ 50 releaseshttps://patch-diff.githubusercontent.com/bactopia/bactopia/releases
Packages 0https://patch-diff.githubusercontent.com/orgs/bactopia/packages?repo_name=bactopia
Please reload this pagehttps://patch-diff.githubusercontent.com/bactopia/bactopia
Please reload this pagehttps://patch-diff.githubusercontent.com/bactopia/bactopia
Contributors 13https://patch-diff.githubusercontent.com/bactopia/bactopia/graphs/contributors
Please reload this pagehttps://patch-diff.githubusercontent.com/bactopia/bactopia
Nextflow 63.1% https://patch-diff.githubusercontent.com/bactopia/bactopia/search?l=nextflow
Perl 14.6% https://patch-diff.githubusercontent.com/bactopia/bactopia/search?l=perl
Python 11.0% https://patch-diff.githubusercontent.com/bactopia/bactopia/search?l=python
Groovy 9.7% https://patch-diff.githubusercontent.com/bactopia/bactopia/search?l=groovy
Shell 1.6% https://patch-diff.githubusercontent.com/bactopia/bactopia/search?l=shell
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.