René's URL Explorer Experiment


Title: GitHub - LooseLab/readfish: CLI tool for flexible and fast adaptive sampling on ONT sequencers

Open Graph Title: GitHub - LooseLab/readfish: CLI tool for flexible and fast adaptive sampling on ONT sequencers

X Title: GitHub - LooseLab/readfish: CLI tool for flexible and fast adaptive sampling on ONT sequencers

Description: CLI tool for flexible and fast adaptive sampling on ONT sequencers - LooseLab/readfish

Open Graph Description: CLI tool for flexible and fast adaptive sampling on ONT sequencers - LooseLab/readfish

X Description: CLI tool for flexible and fast adaptive sampling on ONT sequencers - LooseLab/readfish

Opengraph URL: https://github.com/LooseLab/readfish

X: @github

direct link

Domain: patch-diff.githubusercontent.com

route-pattern/:user_id/:repository
route-controllerfiles
route-actiondisambiguate
fetch-noncev2:62f25776-cbb4-9472-8567-cc626c9a3587
current-catalog-service-hashf3abb0cc802f3d7b95fc8762b94bdcb13bf39634c40c357301c4aa1d67a256fb
request-id8500:263ABA:5E1518:7ACCC0:698D20FF
html-safe-nonce8aa1267dd9b311b43e5da1dcf72fcea134a9e3c575dc8cf1ae14b94368e4350d
visitor-payloadeyJyZWZlcnJlciI6IiIsInJlcXVlc3RfaWQiOiI4NTAwOjI2M0FCQTo1RTE1MTg6N0FDQ0MwOjY5OEQyMEZGIiwidmlzaXRvcl9pZCI6IjUwODM3ODI3NjA4ODA3NDI2NTUiLCJyZWdpb25fZWRnZSI6ImlhZCIsInJlZ2lvbl9yZW5kZXIiOiJpYWQifQ==
visitor-hmacd11818c5ead54283f9a8d6ed3e36eefd80ada05aebefe2edd64e7a43e6ed8f14
hovercard-subject-tagrepository:220492505
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/LooseLab/readfish
twitter:imagehttps://repository-images.githubusercontent.com/220492505/46b6222c-175a-4fe4-a5e3-29fd8618d699
twitter:cardsummary_large_image
og:imagehttps://repository-images.githubusercontent.com/220492505/46b6222c-175a-4fe4-a5e3-29fd8618d699
og:image:altCLI tool for flexible and fast adaptive sampling on ONT sequencers - LooseLab/readfish
og:site_nameGitHub
og:typeobject
hostnamegithub.com
expected-hostnamegithub.com
Nonec25395580e1e3bf82d705e0982a1b24255366088720fef945f1493d5e3e67954
turbo-cache-controlno-preview
go-importgithub.com/LooseLab/readfish git https://github.com/LooseLab/readfish.git
octolytics-dimension-user_id8957500
octolytics-dimension-user_loginLooseLab
octolytics-dimension-repository_id220492505
octolytics-dimension-repository_nwoLooseLab/readfish
octolytics-dimension-repository_publictrue
octolytics-dimension-repository_is_forkfalse
octolytics-dimension-repository_network_root_id220492505
octolytics-dimension-repository_network_root_nwoLooseLab/readfish
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
release94219dcb9c044792ec271fd5b23c73419858bef7
ui-targetfull
theme-color#1e2327
color-schemelight dark

Links:

Skip to contenthttps://patch-diff.githubusercontent.com/LooseLab/readfish#start-of-content
https://patch-diff.githubusercontent.com/
Sign in https://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2FLooseLab%2Freadfish
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%2FLooseLab%2Freadfish
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=LooseLab%2Freadfish
Reloadhttps://patch-diff.githubusercontent.com/LooseLab/readfish
Reloadhttps://patch-diff.githubusercontent.com/LooseLab/readfish
Reloadhttps://patch-diff.githubusercontent.com/LooseLab/readfish
LooseLab https://patch-diff.githubusercontent.com/LooseLab
readfishhttps://patch-diff.githubusercontent.com/LooseLab/readfish
Notifications https://patch-diff.githubusercontent.com/login?return_to=%2FLooseLab%2Freadfish
Fork 35 https://patch-diff.githubusercontent.com/login?return_to=%2FLooseLab%2Freadfish
Star 193 https://patch-diff.githubusercontent.com/login?return_to=%2FLooseLab%2Freadfish
looselab.github.io/readfish/https://looselab.github.io/readfish/
GPL-3.0 license https://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/LICENSE
193 stars https://patch-diff.githubusercontent.com/LooseLab/readfish/stargazers
35 forks https://patch-diff.githubusercontent.com/LooseLab/readfish/forks
Branches https://patch-diff.githubusercontent.com/LooseLab/readfish/branches
Tags https://patch-diff.githubusercontent.com/LooseLab/readfish/tags
Activity https://patch-diff.githubusercontent.com/LooseLab/readfish/activity
Star https://patch-diff.githubusercontent.com/login?return_to=%2FLooseLab%2Freadfish
Notifications https://patch-diff.githubusercontent.com/login?return_to=%2FLooseLab%2Freadfish
Code https://patch-diff.githubusercontent.com/LooseLab/readfish
Issues 16 https://patch-diff.githubusercontent.com/LooseLab/readfish/issues
Pull requests 0 https://patch-diff.githubusercontent.com/LooseLab/readfish/pulls
Discussions https://patch-diff.githubusercontent.com/LooseLab/readfish/discussions
Actions https://patch-diff.githubusercontent.com/LooseLab/readfish/actions
Projects 1 https://patch-diff.githubusercontent.com/LooseLab/readfish/projects
Wiki https://patch-diff.githubusercontent.com/LooseLab/readfish/wiki
Security 0 https://patch-diff.githubusercontent.com/LooseLab/readfish/security
Insights https://patch-diff.githubusercontent.com/LooseLab/readfish/pulse
Code https://patch-diff.githubusercontent.com/LooseLab/readfish
Issues https://patch-diff.githubusercontent.com/LooseLab/readfish/issues
Pull requests https://patch-diff.githubusercontent.com/LooseLab/readfish/pulls
Discussions https://patch-diff.githubusercontent.com/LooseLab/readfish/discussions
Actions https://patch-diff.githubusercontent.com/LooseLab/readfish/actions
Projects https://patch-diff.githubusercontent.com/LooseLab/readfish/projects
Wiki https://patch-diff.githubusercontent.com/LooseLab/readfish/wiki
Security https://patch-diff.githubusercontent.com/LooseLab/readfish/security
Insights https://patch-diff.githubusercontent.com/LooseLab/readfish/pulse
Brancheshttps://patch-diff.githubusercontent.com/LooseLab/readfish/branches
Tagshttps://patch-diff.githubusercontent.com/LooseLab/readfish/tags
https://patch-diff.githubusercontent.com/LooseLab/readfish/branches
https://patch-diff.githubusercontent.com/LooseLab/readfish/tags
407 Commitshttps://patch-diff.githubusercontent.com/LooseLab/readfish/commits/main/
https://patch-diff.githubusercontent.com/LooseLab/readfish/commits/main/
.githubhttps://patch-diff.githubusercontent.com/LooseLab/readfish/tree/main/.github
.githubhttps://patch-diff.githubusercontent.com/LooseLab/readfish/tree/main/.github
docshttps://patch-diff.githubusercontent.com/LooseLab/readfish/tree/main/docs
docshttps://patch-diff.githubusercontent.com/LooseLab/readfish/tree/main/docs
src/readfishhttps://patch-diff.githubusercontent.com/LooseLab/readfish/tree/main/src/readfish
src/readfishhttps://patch-diff.githubusercontent.com/LooseLab/readfish/tree/main/src/readfish
testshttps://patch-diff.githubusercontent.com/LooseLab/readfish/tree/main/tests
testshttps://patch-diff.githubusercontent.com/LooseLab/readfish/tree/main/tests
.gitignorehttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/.gitignore
.gitignorehttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/.gitignore
.pre-commit-config.yamlhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/.pre-commit-config.yaml
.pre-commit-config.yamlhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/.pre-commit-config.yaml
CITATION.cffhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/CITATION.cff
CITATION.cffhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/CITATION.cff
LICENSEhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/LICENSE
LICENSEhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/LICENSE
README.mdhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/README.md
README.mdhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/README.md
_statichttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/_static
_statichttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/_static
pyproject.tomlhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/pyproject.toml
pyproject.tomlhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/pyproject.toml
READMEhttps://patch-diff.githubusercontent.com/LooseLab/readfish
Contributinghttps://patch-diff.githubusercontent.com/LooseLab/readfish
GPL-3.0 licensehttps://patch-diff.githubusercontent.com/LooseLab/readfish
https://github.com/LooseLab/readfish/blob/main/docs/_static/readfish_logo.jpg?raw=true
list of GOTCHAshttps://patch-diff.githubusercontent.com/LooseLab/readfish#common-gotchas
https://looselab.github.io/readfishhttps://looselab.github.io/readfish
FAQhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/docs/FAQ.md
Read Until APIhttps://github.com/nanoporetech/read_until_api
https://patch-diff.githubusercontent.com/LooseLab/readfish#supported-sequencing-platforms
herehttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/docs/toml.md#aligner
https://patch-diff.githubusercontent.com/LooseLab/readfish#supported-oss
https://patch-diff.githubusercontent.com/LooseLab/readfish#citation
nature biotechnologyhttps://dx.doi.org/10.1038/s41587-020-00746-x
bioRxivhttps://dx.doi.org/10.1101/2020.02.03.926956
10.1038/s41587-020-00746-xhttps://dx.doi.org/10.1038/s41587-020-00746-x
https://doi.org/10.1038/s41587-020-00746-xhttps://doi.org/10.1038/s41587-020-00746-x
https://patch-diff.githubusercontent.com/LooseLab/readfish#other-works
bioRxivhttps://www.biorxiv.org/content/10.1101/2021.12.01.470722v1
https://doi.org/10.1101/2021.12.01.470722https://doi.org/10.1101/2021.12.01.470722
https://patch-diff.githubusercontent.com/LooseLab/readfish#installation
condahttps://conda.io
https://patch-diff.githubusercontent.com/LooseLab/readfish#apple-silicon
https://patch-diff.githubusercontent.com/LooseLab/readfish#installing-with-development-dependencies
development.ymlhttps://github.com/LooseLab/readfish/blob/e30f1fa8ac7a37bb39e9d8b49251426fe1674c98/docs/development.yml
https://patch-diff.githubusercontent.com/LooseLab/readfish#️-important--
issuehttps://github.com/LooseLab/readfish/issues/221#issuecomment-1381529409
ONT's Dorado Basecall Server GPUhttps://community.nanoporetech.com/downloads
https://patch-diff.githubusercontent.com/LooseLab/readfish#usage
https://patch-diff.githubusercontent.com/LooseLab/readfish#toml-file
TOML.mdhttps://patch-diff.githubusercontent.com/LooseLab/readfish/blob/main/docs/toml.md
TOML file herehttps://github.com//LooseLab/readfish/tree/main/docs/_static/example_tomls
https://patch-diff.githubusercontent.com/LooseLab/readfish#testing
https://patch-diff.githubusercontent.com/LooseLab/readfish#adding-a-simulated-position-for-testing
https://patch-diff.githubusercontent.com/LooseLab/readfish#configuring-bulk-fast5-file-playback
R9.4.1 4khzhttps://s3.amazonaws.com/nanopore-human-wgs/bulkfile/PLSP57501_20170308_FNFAF14035_MN16458_sequencing_run_NOTT_Hum_wh1rs2_60428.fast5
R10 (5khz)https://s3.amazonaws.com/nanopore-human-wgs/bulkfile/GXB02001_20230509_1250_FAW79338_X3_sequencing_run_NA12878_B1_19382aa5_ef4362cd.fast5
R10.4 4khzhttps://s3.amazonaws.com/nanopore-human-wgs/bulkfile/PC24B243_20220512_1516_PAK21362_3H_sequencing_run_NA12878_sheared20kb_3d5147fc.fast5
https://github.com/LooseLab/readfish/blob/247185a1bdcbe1275c55a6b4b1e2c7273213af91/docs/_static/images/simulated_playback_run_options.png?raw=true
https://patch-diff.githubusercontent.com/LooseLab/readfish#old-method-configuring-bulk-fast5-file-playback
R9.4.1https://s3.amazonaws.com/nanopore-human-wgs/bulkfile/PLSP57501_20170308_FNFAF14035_MN16458_sequencing_run_NOTT_Hum_wh1rs2_60428.fast5
R10 (5khz)https://s3.amazonaws.com/nanopore-human-wgs/bulkfile/GXB02001_20230509_1250_FAW79338_X3_sequencing_run_NA12878_B1_19382aa5_ef4362cd.fast5
R10.4, 4khzhttps://s3.amazonaws.com/nanopore-human-wgs/bulkfile/PC24B243_20220512_1516_PAK21362_3H_sequencing_run_NA12878_sheared20kb_3d5147fc.fast5
https://github.com/LooseLab/readfish/raw/main/docs/_static/images/PlaybackControlRun30Minutes.png?raw=true
https://patch-diff.githubusercontent.com/LooseLab/readfish#testing-unblock-response
https://github.com/LooseLab/readfish/raw/main/docs/_static/images/PlaybackUnblockAll30minutes.png?raw=true
https://github.com/LooseLab/readfish/raw/main/docs/_static/images/PlaybackUnblockAllCloseUp.png?raw=true
https://patch-diff.githubusercontent.com/LooseLab/readfish#testing-base-calling-and-mapping
dorado basecall serverhttps://community.nanoporetech.com/downloads/dorado/release_notes
minimap2https://github.com/lh3/minimap2
https://patch-diff.githubusercontent.com/LooseLab/readfish#testing-expected-results-from-a-selection-experiment
https://github.com/LooseLab/readfish/raw/main/docs/_static/images/PlaybackRunTargeted.png?raw=true
https://github.com/LooseLab/readfish/raw/main/docs/_static/images/PlaybackRunTargetedUnblockPeak.png?raw=true
https://github.com/LooseLab/readfish/raw/main/docs/_static/images/PlaybackRunTargetedPeak.png?raw=true
https://patch-diff.githubusercontent.com/LooseLab/readfish#analysing-results-with-readfish-stats
https://patch-diff.githubusercontent.com/LooseLab/readfish#common-gotchas
https://patch-diff.githubusercontent.com/LooseLab/readfish#acknowledgements
@tim_bassfordhttps://twitter.com/tim_bassford
@TurbineCreativehttps://twitter.com/TurbineCreative
https://patch-diff.githubusercontent.com/LooseLab/readfish#changelog
https://patch-diff.githubusercontent.com/LooseLab/readfish#202430
https://patch-diff.githubusercontent.com/LooseLab/readfish#this-release-is-breaking-for-all-versions-of-minknow--6-and-no-longer-supports-guppy
https://patch-diff.githubusercontent.com/LooseLab/readfish#202420
#347https://github.com/LooseLab/readfish/issues/347
(#344)https://github.com/LooseLab/readfish/pull/344
(#351)https://github.com/LooseLab/readfish/pull/351
https://patch-diff.githubusercontent.com/LooseLab/readfish#202410
(#327)https://github.com/LooseLab/readfish/pull/327
(#323)https://github.com/LooseLab/readfish/pull/323
(#330)https://github.com/LooseLab/readfish/pull/330
(#313)https://github.com/LooseLab/readfish/pull/313
(#324)https://github.com/LooseLab/readfish/pull/324
https://patch-diff.githubusercontent.com/LooseLab/readfish#202311
looselab.github.io/readfish/https://looselab.github.io/readfish/
bioinformatics https://patch-diff.githubusercontent.com/topics/bioinformatics
genomics https://patch-diff.githubusercontent.com/topics/genomics
sequencing https://patch-diff.githubusercontent.com/topics/sequencing
oxford-nanopore https://patch-diff.githubusercontent.com/topics/oxford-nanopore
ont https://patch-diff.githubusercontent.com/topics/ont
adaptive-sampling https://patch-diff.githubusercontent.com/topics/adaptive-sampling
Readme https://patch-diff.githubusercontent.com/LooseLab/readfish#readme-ov-file
GPL-3.0 license https://patch-diff.githubusercontent.com/LooseLab/readfish#GPL-3.0-1-ov-file
Contributing https://patch-diff.githubusercontent.com/LooseLab/readfish#contributing-ov-file
Please reload this pagehttps://patch-diff.githubusercontent.com/LooseLab/readfish
Activityhttps://patch-diff.githubusercontent.com/LooseLab/readfish/activity
Custom propertieshttps://patch-diff.githubusercontent.com/LooseLab/readfish/custom-properties
193 starshttps://patch-diff.githubusercontent.com/LooseLab/readfish/stargazers
13 watchinghttps://patch-diff.githubusercontent.com/LooseLab/readfish/watchers
35 forkshttps://patch-diff.githubusercontent.com/LooseLab/readfish/forks
Report repository https://patch-diff.githubusercontent.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2FLooseLab%2Freadfish&report=LooseLab+%28user%29
Releases 8https://patch-diff.githubusercontent.com/LooseLab/readfish/releases
v2024.3.0 MinKNOW 6.0 compatibilty, pass reads and bug fixes Latest Sep 12, 2024 https://patch-diff.githubusercontent.com/LooseLab/readfish/releases/tag/v2024.3.0
+ 7 releaseshttps://patch-diff.githubusercontent.com/LooseLab/readfish/releases
Please reload this pagehttps://patch-diff.githubusercontent.com/LooseLab/readfish
Contributors 5https://patch-diff.githubusercontent.com/LooseLab/readfish/graphs/contributors
Please reload this pagehttps://patch-diff.githubusercontent.com/LooseLab/readfish
Python 100.0% https://patch-diff.githubusercontent.com/LooseLab/readfish/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.