{"id":26329166,"url":"https://github.com/murrellgroup/robustamplicondenoising.jl","last_synced_at":"2025-08-27T11:19:12.469Z","repository":{"id":70649759,"uuid":"143098864","full_name":"MurrellGroup/RobustAmpliconDenoising.jl","owner":"MurrellGroup","description":"RobustAmpliconDenoising.jl: ","archived":false,"fork":false,"pushed_at":"2025-03-26T14:24:09.000Z","size":1007,"stargazers_count":6,"open_issues_count":1,"forks_count":1,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-03-26T15:38:24.919Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://murrellgroup.github.io/RobustAmpliconDenoising.jl/","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MurrellGroup.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-08-01T03:24:43.000Z","updated_at":"2025-03-26T14:24:13.000Z","dependencies_parsed_at":"2025-03-26T15:29:15.159Z","dependency_job_id":"f7c271e4-0d25-4359-8eab-4ae87e0f4270","html_url":"https://github.com/MurrellGroup/RobustAmpliconDenoising.jl","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/MurrellGroup/RobustAmpliconDenoising.jl","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MurrellGroup%2FRobustAmpliconDenoising.jl","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MurrellGroup%2FRobustAmpliconDenoising.jl/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MurrellGroup%2FRobustAmpliconDenoising.jl/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MurrellGroup%2FRobustAmpliconDenoising.jl/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MurrellGroup","download_url":"https://codeload.github.com/MurrellGroup/RobustAmpliconDenoising.jl/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MurrellGroup%2FRobustAmpliconDenoising.jl/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272325441,"owners_count":24914642,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-27T02:00:09.397Z","response_time":76,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-03-15T21:19:39.807Z","updated_at":"2025-08-27T11:19:12.457Z","avatar_url":"https://github.com/MurrellGroup.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Robust Amplicon Denoising\nThis is the repository for the Robust Amplicon Denoising tool, which is suitable for denoising very long PacBio amplicon reads with relatively high error rates. Note that FAD is now available from within the NextGenSeqUtils.jl package.\n\n## Note: This package is not registered. To install this package, along with its dependencies, please use the following:\n```julia \nusing Pkg\nPkg.add(url=\"https://github.com/MurrellGroup/NextGenSeqUtils.jl\")\nPkg.add(url=\"https://github.com/MurrellGroup/DPMeansClustering.jl\")\nPkg.add(url=\"https://github.com/MurrellGroup/RobustAmpliconDenoising.jl\")\n```\n\n## Getting started quickly:\nLoad the package:\n```julia\nusing NextGenSeqUtils, RobustAmpliconDenoising\n```\nThe run, via:\n```julia\nseqs, QVs, seq_names = read_fastq(\"someInputFile.fastq\")\ntemplates,template_sizes,template_indices = denoise(seqs)\nwrite_fasta(\"someOutputFile.fasta\",templates,names = [\"seq$(j)_$(template_sizes[j])\" for j in 1:length(template_sizes)])\n```\n\n## But...\nYou likely want to filter your reads by length, and by expected error rate. Also, PacBio reads come in random orientations, and you probably want to figure out how they should be oriented.\n\nFor an example for how to orient using primers, see: https://nextjournal.com/Murrell-Lab/scfv-fad-analysis/\n\n## DOCS\nhttps://murrellgroup.github.io/RobustAmpliconDenoising.jl/\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmurrellgroup%2Frobustamplicondenoising.jl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmurrellgroup%2Frobustamplicondenoising.jl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmurrellgroup%2Frobustamplicondenoising.jl/lists"}