René's URL Explorer Experiment

Title: GitHub - ozankiratli/PoolSeqFlow: A Nextflow pipeline for allele frequency analysis from pooled Illumina sequencing data · GitHub

Open Graph Title: GitHub - ozankiratli/PoolSeqFlow: A Nextflow pipeline for allele frequency analysis from pooled Illumina sequencing data

X Title: GitHub - ozankiratli/PoolSeqFlow: A Nextflow pipeline for allele frequency analysis from pooled Illumina sequencing data

Description: A Nextflow pipeline for allele frequency analysis from pooled Illumina sequencing data - ozankiratli/PoolSeqFlow

Open Graph Description: A Nextflow pipeline for allele frequency analysis from pooled Illumina sequencing data - ozankiratli/PoolSeqFlow

X Description: A Nextflow pipeline for allele frequency analysis from pooled Illumina sequencing data - ozankiratli/PoolSeqFlow

Opengraph URL: https://github.com/ozankiratli/PoolSeqFlow

X: @github

direct link

Domain: github.com

route-pattern	/:user_id/:repository
route-controller	files
route-action	disambiguate
fetch-nonce	v2:004ce598-001a-2fbb-22a3-50060129d78b
current-catalog-service-hash	f3abb0cc802f3d7b95fc8762b94bdcb13bf39634c40c357301c4aa1d67a256fb
request-id	8134:24568D:9A3745:D04922:6A4C47E3
html-safe-nonce	3a241850f1a787f3e7ee4ece68b1c86d7c4a4b9eab1b3407761bdce1b0f55e69
visitor-payload	eyJyZWZlcnJlciI6IiIsInJlcXVlc3RfaWQiOiI4MTM0OjI0NTY4RDo5QTM3NDU6RDA0OTIyOjZBNEM0N0UzIiwidmlzaXRvcl9pZCI6Ijg3NDA1NjkxODE0MzczMTUwNDMiLCJyZWdpb25fZWRnZSI6ImlhZCIsInJlZ2lvbl9yZW5kZXIiOiJpYWQifQ==
visitor-hmac	4769f9c9d394fcb6b987a107ff844fb89ee0f50aabeef8cdcc7ed88be9db487b
hovercard-subject-tag	repository:1180986339
github-keyboard-shortcuts	repository,copilot
google-site-verification	Apib7-x98H0j5cPqHWwSMm6dNU4GmODRoqxLiDzdx9I
octolytics-url	https://collector.github.com/github/collect
analytics-location	//
fb:app_id	1401488693436528
apple-itunes-app	app-id=1477376905, app-argument=https://github.com/ozankiratli/PoolSeqFlow
twitter:image	https://opengraph.githubassets.com/09f5909c91209b8bd3ad795555a8c6ff5112de50067a174622585f586205ddc9/ozankiratli/PoolSeqFlow
twitter:card	summary_large_image
og:image	https://opengraph.githubassets.com/09f5909c91209b8bd3ad795555a8c6ff5112de50067a174622585f586205ddc9/ozankiratli/PoolSeqFlow
og:image:alt	A Nextflow pipeline for allele frequency analysis from pooled Illumina sequencing data - ozankiratli/PoolSeqFlow
og:image:width	1200
og:image:height	600
og:site_name	GitHub
og:type	object
hostname	github.com
expected-hostname	github.com
None	3d11bb817438277de2a940854450e83a7d32b6aeb5014e9e6b00a6423900251c
turbo-cache-control	no-cache
go-import	github.com/ozankiratli/PoolSeqFlow git https://github.com/ozankiratli/PoolSeqFlow.git
octolytics-dimension-user_id	18036138
octolytics-dimension-user_login	ozankiratli
octolytics-dimension-repository_id	1180986339
octolytics-dimension-repository_nwo	ozankiratli/PoolSeqFlow
octolytics-dimension-repository_public	true
octolytics-dimension-repository_is_fork	false
octolytics-dimension-repository_network_root_id	1180986339
octolytics-dimension-repository_network_root_nwo	ozankiratli/PoolSeqFlow
turbo-body-classes	logged-out env-production page-responsive
disable-turbo	false
browser-stats-url	https://api.github.com/_private/browser/stats
browser-errors-url	https://api.github.com/_private/browser/errors
release	3996b3b83990e134be6c099ab9a7f48f140ae80f
ui-target	full
theme-color	#1e2327
color-scheme	light dark

Links:

Skip to content	https://github.com/ozankiratli/PoolSeqFlow#start-of-content
	https://github.com/
Sign in	https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fozankiratli%2FPoolSeqFlow
GitHub CopilotWrite better code with AI	https://github.com/features/copilot
GitHub Copilot appDirect agents from issue to merge	https://github.com/features/ai/github-app
MCP RegistryNewIntegrate external tools	https://github.com/mcp
ActionsAutomate any workflow	https://github.com/features/actions
CodespacesInstant dev environments	https://github.com/features/codespaces
IssuesPlan and track work	https://github.com/features/issues
Code ReviewManage code changes	https://github.com/features/code-review
GitHub Advanced SecurityFind and fix vulnerabilities	https://github.com/security/advanced-security
Code securitySecure your code as you build	https://github.com/security/advanced-security/code-security
Secret protectionStop leaks before they start	https://github.com/security/advanced-security/secret-protection
Why GitHub	https://github.com/why-github
Documentation	https://docs.github.com
Blog	https://github.blog
Changelog	https://github.blog/changelog
Marketplace	https://github.com/marketplace
View all features	https://github.com/features
Enterprises	https://github.com/enterprise
Small and medium teams	https://github.com/team
Startups	https://github.com/enterprise/startups
Nonprofits	https://github.com/solutions/industry/nonprofits
App Modernization	https://github.com/solutions/use-case/app-modernization
DevSecOps	https://github.com/solutions/use-case/devsecops
DevOps	https://github.com/solutions/use-case/devops
CI/CD	https://github.com/solutions/use-case/ci-cd
View all use cases	https://github.com/solutions/use-case
Healthcare	https://github.com/solutions/industry/healthcare
Financial services	https://github.com/solutions/industry/financial-services
Manufacturing	https://github.com/solutions/industry/manufacturing
Government	https://github.com/solutions/industry/government
View all industries	https://github.com/solutions/industry
View all solutions	https://github.com/solutions
AI	https://github.com/resources/articles?topic=ai
Software Development	https://github.com/resources/articles?topic=software-development
DevOps	https://github.com/resources/articles?topic=devops
Security	https://github.com/resources/articles?topic=security
View all topics	https://github.com/resources/articles
Customer stories	https://github.com/customer-stories
Events & webinars	https://github.com/resources/events
Ebooks & reports	https://github.com/resources/whitepapers
Business insights	https://github.com/solutions/executive-insights
GitHub Skills	https://skills.github.com
Documentation	https://docs.github.com
Customer support	https://support.github.com
Community forum	https://github.com/orgs/community/discussions
Trust center	https://github.com/trust-center
Partners	https://github.com/partners
View all resources	https://github.com/resources
GitHub SponsorsFund open source developers	https://github.com/sponsors
Security Lab	https://securitylab.github.com
Maintainer Community	https://maintainers.github.com
Accelerator	https://github.com/accelerator
GitHub Stars	https://stars.github.com
Archive Program	https://archiveprogram.github.com
Topics	https://github.com/topics
Trending	https://github.com/trending
Collections	https://github.com/collections
Enterprise platformAI-powered developer platform	https://github.com/enterprise
GitHub Advanced SecurityEnterprise-grade security features	https://github.com/security/advanced-security
Copilot for BusinessEnterprise-grade AI features	https://github.com/features/copilot/copilot-business
Premium SupportEnterprise-grade 24/7 support	https://github.com/premium-support
Pricing	https://github.com/pricing
Search syntax tips	https://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
documentation	https://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%2Fozankiratli%2FPoolSeqFlow
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=ozankiratli%2FPoolSeqFlow
Reload	https://github.com/ozankiratli/PoolSeqFlow
Reload	https://github.com/ozankiratli/PoolSeqFlow
Reload	https://github.com/ozankiratli/PoolSeqFlow
ozankiratli	https://github.com/ozankiratli
PoolSeqFlow	https://github.com/ozankiratli/PoolSeqFlow
Notifications	https://github.com/login?return_to=%2Fozankiratli%2FPoolSeqFlow
Fork 0	https://github.com/login?return_to=%2Fozankiratli%2FPoolSeqFlow
Star 1	https://github.com/login?return_to=%2Fozankiratli%2FPoolSeqFlow
Code	https://github.com/ozankiratli/PoolSeqFlow
Issues 0	https://github.com/ozankiratli/PoolSeqFlow/issues
Pull requests 0	https://github.com/ozankiratli/PoolSeqFlow/pulls
Actions	https://github.com/ozankiratli/PoolSeqFlow/actions
Projects	https://github.com/ozankiratli/PoolSeqFlow/projects
Security and quality 0	https://github.com/ozankiratli/PoolSeqFlow/security
Insights	https://github.com/ozankiratli/PoolSeqFlow/pulse
Code	https://github.com/ozankiratli/PoolSeqFlow
Issues	https://github.com/ozankiratli/PoolSeqFlow/issues
Pull requests	https://github.com/ozankiratli/PoolSeqFlow/pulls
Actions	https://github.com/ozankiratli/PoolSeqFlow/actions
Projects	https://github.com/ozankiratli/PoolSeqFlow/projects
Security and quality	https://github.com/ozankiratli/PoolSeqFlow/security
Insights	https://github.com/ozankiratli/PoolSeqFlow/pulse
	https://github.com/ozankiratli/PoolSeqFlow
Branches	https://github.com/ozankiratli/PoolSeqFlow/branches
Tags	https://github.com/ozankiratli/PoolSeqFlow/tags
	https://github.com/ozankiratli/PoolSeqFlow/branches
	https://github.com/ozankiratli/PoolSeqFlow/tags
9 Commits	https://github.com/ozankiratli/PoolSeqFlow/commits/main/
	https://github.com/ozankiratli/PoolSeqFlow/commits/main/
bin	https://github.com/ozankiratli/PoolSeqFlow/tree/main/bin
bin	https://github.com/ozankiratli/PoolSeqFlow/tree/main/bin
install	https://github.com/ozankiratli/PoolSeqFlow/tree/main/install
install	https://github.com/ozankiratli/PoolSeqFlow/tree/main/install
scripts	https://github.com/ozankiratli/PoolSeqFlow/tree/main/scripts
scripts	https://github.com/ozankiratli/PoolSeqFlow/tree/main/scripts
.gitignore	https://github.com/ozankiratli/PoolSeqFlow/blob/main/.gitignore
.gitignore	https://github.com/ozankiratli/PoolSeqFlow/blob/main/.gitignore
CHANGELOG.md	https://github.com/ozankiratli/PoolSeqFlow/blob/main/CHANGELOG.md
CHANGELOG.md	https://github.com/ozankiratli/PoolSeqFlow/blob/main/CHANGELOG.md
LICENSE	https://github.com/ozankiratli/PoolSeqFlow/blob/main/LICENSE
LICENSE	https://github.com/ozankiratli/PoolSeqFlow/blob/main/LICENSE
PoolSeqFlow	https://github.com/ozankiratli/PoolSeqFlow/blob/main/PoolSeqFlow
PoolSeqFlow	https://github.com/ozankiratli/PoolSeqFlow/blob/main/PoolSeqFlow
README.md	https://github.com/ozankiratli/PoolSeqFlow/blob/main/README.md
README.md	https://github.com/ozankiratli/PoolSeqFlow/blob/main/README.md
README.old	https://github.com/ozankiratli/PoolSeqFlow/blob/main/README.old
README.old	https://github.com/ozankiratli/PoolSeqFlow/blob/main/README.old
RGTags.csv.template	https://github.com/ozankiratli/PoolSeqFlow/blob/main/RGTags.csv.template
RGTags.csv.template	https://github.com/ozankiratli/PoolSeqFlow/blob/main/RGTags.csv.template
nextflow.config	https://github.com/ozankiratli/PoolSeqFlow/blob/main/nextflow.config
nextflow.config	https://github.com/ozankiratli/PoolSeqFlow/blob/main/nextflow.config
parameters.config	https://github.com/ozankiratli/PoolSeqFlow/blob/main/parameters.config
parameters.config	https://github.com/ozankiratli/PoolSeqFlow/blob/main/parameters.config
parameters.config.template	https://github.com/ozankiratli/PoolSeqFlow/blob/main/parameters.config.template
parameters.config.template	https://github.com/ozankiratli/PoolSeqFlow/blob/main/parameters.config.template
poolseqflow.nf	https://github.com/ozankiratli/PoolSeqFlow/blob/main/poolseqflow.nf
poolseqflow.nf	https://github.com/ozankiratli/PoolSeqFlow/blob/main/poolseqflow.nf
README	https://github.com/ozankiratli/PoolSeqFlow
Apache-2.0 license	https://github.com/ozankiratli/PoolSeqFlow
	https://github.com/ozankiratli/PoolSeqFlow#poolseqflow
	https://www.nextflow.io/
	https://opensource.org/licenses/Apache-2.0
	https://doi.org/10.5281/zenodo.19245612
	https://github.com/ozankiratli/PoolSeqFlow#overview
	https://github.com/ozankiratli/PoolSeqFlow#pipeline-overview
	https://github.com/ozankiratli/PoolSeqFlow#features
Step 7	https://github.com/ozankiratli/PoolSeqFlow#step-7-vcf--allele-frequency-tables
Resume Logic	https://github.com/ozankiratli/PoolSeqFlow#resume-logic
	https://github.com/ozankiratli/PoolSeqFlow#requirements
Conda	https://docs.conda.io/en/latest/miniconda.html
	https://github.com/ozankiratli/PoolSeqFlow#quick-start
	https://github.com/ozankiratli/PoolSeqFlow#1-clone-the-repository
	https://github.com/ozankiratli/PoolSeqFlow#2-configure-the-pipeline
RG Tag Configuration	https://github.com/ozankiratli/PoolSeqFlow#rg-tag-configuration
	https://github.com/ozankiratli/PoolSeqFlow#3-install-the-environment
	https://github.com/ozankiratli/PoolSeqFlow#4-run-the-pipeline
	https://github.com/ozankiratli/PoolSeqFlow#5-additional-commands
	https://github.com/ozankiratli/PoolSeqFlow#resume-logic
	https://github.com/ozankiratli/PoolSeqFlow#directory-structure
	https://github.com/ozankiratli/PoolSeqFlow#repository
	https://github.com/ozankiratli/PoolSeqFlow#required-project-directory-layout
	https://github.com/ozankiratli/PoolSeqFlow#output-structure
	https://github.com/ozankiratli/PoolSeqFlow#configuration
	https://github.com/ozankiratli/PoolSeqFlow#resource-configuration
	https://github.com/ozankiratli/PoolSeqFlow#samtools-filter-flags
	https://github.com/ozankiratli/PoolSeqFlow#rg-tag-configuration
	https://github.com/ozankiratli/PoolSeqFlow#step-by-step-description
	https://github.com/ozankiratli/PoolSeqFlow#step-0-verify-environment
	https://github.com/ozankiratli/PoolSeqFlow#step-1-build-reference-dictionaries
	https://github.com/ozankiratli/PoolSeqFlow#step-2-trim--qc
	https://github.com/ozankiratli/PoolSeqFlow#step-3-align
	https://github.com/ozankiratli/PoolSeqFlow#step-4-clean-bam-files
	https://github.com/ozankiratli/PoolSeqFlow#step-5-generate-reports
	https://github.com/ozankiratli/PoolSeqFlow#step-6-variant-calling
	https://github.com/ozankiratli/PoolSeqFlow#step-7-vcf--allele-frequency-tables
	https://github.com/ozankiratli/PoolSeqFlow#step-8-annotate-variants-optional
	https://github.com/ozankiratli/PoolSeqFlow#troubleshooting
	https://github.com/ozankiratli/PoolSeqFlow#citation
https://github.com/ozankiratli/PoolSeqFlow	https://github.com/ozankiratli/PoolSeqFlow
10.5281/zenodo.19245612	https://doi.org/10.5281/zenodo.19245612
	https://github.com/ozankiratli/PoolSeqFlow#license
Apache 2.0 License	https://github.com/ozankiratli/PoolSeqFlow/blob/main/LICENSE
	https://github.com/ozankiratli/PoolSeqFlow#contact
@ozankiratli	https://github.com/ozankiratli
https://github.com/ozankiratli/PoolSeqFlow/issues	https://github.com/ozankiratli/PoolSeqFlow/issues
nextflow	https://github.com/topics/nextflow
illumina	https://github.com/topics/illumina
pool-sequencing	https://github.com/topics/pool-sequencing
nextflow-pipeline	https://github.com/topics/nextflow-pipeline
nextflow-pipelines	https://github.com/topics/nextflow-pipelines
poolseq	https://github.com/topics/poolseq
Readme	https://github.com/ozankiratli/PoolSeqFlow#readme-ov-file
Apache-2.0 license	https://github.com/ozankiratli/PoolSeqFlow#Apache-2.0-1-ov-file
Please reload this page	https://github.com/ozankiratli/PoolSeqFlow
Activity	https://github.com/ozankiratli/PoolSeqFlow/activity
0 forks	https://github.com/ozankiratli/PoolSeqFlow/forks
Report repository	https://github.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2Fozankiratli%2FPoolSeqFlow&report=ozankiratli+%28user%29
Releases 2	https://github.com/ozankiratli/PoolSeqFlow/releases
v1.0.1 Latest Jun 3, 2026	https://github.com/ozankiratli/PoolSeqFlow/releases/tag/v1.0.1
+ 1 release	https://github.com/ozankiratli/PoolSeqFlow/releases
Packages 0	https://github.com/users/ozankiratli/packages?repo_name=PoolSeqFlow
Please reload this page	https://github.com/ozankiratli/PoolSeqFlow
Contributors	https://github.com/ozankiratli/PoolSeqFlow/graphs/contributors
Please reload this page	https://github.com/ozankiratli/PoolSeqFlow
Nextflow 85.8%	https://github.com/ozankiratli/PoolSeqFlow/search?l=nextflow
Shell 7.0%	https://github.com/ozankiratli/PoolSeqFlow/search?l=shell
Python 5.8%	https://github.com/ozankiratli/PoolSeqFlow/search?l=python
Awk 1.4%	https://github.com/ozankiratli/PoolSeqFlow/search?l=awk
	https://github.com
Terms	https://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacy	https://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Security	https://github.com/security
Status	https://www.githubstatus.com/
Community	https://github.community/
Docs	https://docs.github.com/
Contact	https://support.github.com?tags=dotcom-footer

Viewport: width=device-width

URLs of crawlers that visited me.