{"id":20153580,"url":"https://github.com/seqan/mason","last_synced_at":"2026-03-06T15:32:27.751Z","repository":{"id":165984005,"uuid":"641349103","full_name":"seqan/mason","owner":"seqan","description":"Tools for Biological Sequence Simulation","archived":false,"fork":false,"pushed_at":"2023-05-17T14:50:56.000Z","size":6762,"stargazers_count":8,"open_issues_count":2,"forks_count":4,"subscribers_count":5,"default_branch":"main","last_synced_at":"2026-02-11T02:26:33.546Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","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/seqan.png","metadata":{"files":{"readme":"README.mason_frag_sequencing.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2023-05-16T09:35:47.000Z","updated_at":"2026-01-02T08:56:43.000Z","dependencies_parsed_at":"2024-08-21T02:15:24.476Z","dependency_job_id":null,"html_url":"https://github.com/seqan/mason","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/seqan/mason","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fmason","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fmason/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fmason/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fmason/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/seqan","download_url":"https://codeload.github.com/seqan/mason/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fmason/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30183473,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-06T14:42:24.748Z","status":"ssl_error","status_checked_at":"2026-03-06T14:42:14.925Z","response_time":250,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2024-11-13T23:19:47.847Z","updated_at":"2026-03-06T15:32:27.716Z","avatar_url":"https://github.com/seqan.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Mason Fragment Sequencing\n## Overview\n\nThe program `mason_frag_sequencing` is a simple sequence simulator.  Instead of the\nend-to-end read simulator `mason_simulator`, the program\n`mason_frag_sequencing` expects as the input DNA fragment.  For these\nfragments, sequencing is then simulated either from one or both ends.\n\nThe program thus exposes the NGS sequencing engine of the Mason package\nwithout fragment selection and variant simulation.\n\n## Examples\n### Help\nThe command:\n```\n  $ mason_frag_sequencing --help\n```\nprints the help for Mason Genome.\n\n### Simulating Paired-End Reads from Fragments\n\nWe call `mason_frag_sequencing` on the file adeno_fragments.fa to simulate\npaired-end Illumina reads (default) of length 100.\n```\n  $ head adeno_fragments.fa\n  \u003efragment0\n  CCTATCTAATAATATACCTTATACTGGACTAGTGCCAATATTAAAATGAAGTGGGCGTAGTGTGTAATTT\n  GATTGGGTGGAGGTGTGGCTTTGGCGTGCTTGTAAGTTTGGGCGGATGAGGAAGTGGGGCGCGGCGTGGG\n  AGCCGGGCGCGCCGGATGTGACGTTTTAGACGCCATTTTACACGGAAATGATGTTTTTTGGGCGTTGTTT\n  GTGCAAATTTTGTGTTTTAGGCGCGAAAACTGAAATGCGGAAGTGAAAATTGATGACGGCAATTTTATTA\n  TAGGC\n  \u003efragment1\n  ACGGGGAAACTCCACGTTGGCGCTCAAAGGGCGCGTTTATTGTTCTGTCAGCTGATCGTTTGGGTATTTA\n  ATGCCGCCGTGTTCGTCAAGAGGCCACTCTTGAGTGCCAGCGAGAAGAGTTTTCTCTGCCAGCTCATTTT\n  CACGGCGCCATTATGAGAACTGAAATGACTCCCTTGGTCCTGTCGTATCAGGAAGCTGACGACATATTGG\n  $ mason_frag_sequencing -i adeno_fragments.fa -o left.fq -or right.fq\n  ...\n  $ head left.fq \n  @simulated.1\n  GCCTATAATAAAATTGCCGTCATCAATTTTCACTTCCGCATTTCAGTTTTCGCGCCTAAAACACAAAATTTGCACAAACAACGCCCAAAAAACATCATTT\n  +\n  IIIHHIHIHIIIIIHHHHIIHGIGGIIIHIGIIFGEIIICGIHHIFFIEIFIHCHFFEIIEHFHIIHIAIIDDIGIHIIIHIIHFIIDBFHDHIIIAIDI\n  @simulated.2\n  GGCAACTCTGGATGGTCTAACTGAAACTCCTCACGTTCCCTATCAGCGGCAGCAGCAGCTGCGGATGCAGAAACATGCGCCATTCCGTTCTCGTCTTGCT\n  +\n  IHIIHIHHIHIIIHHHHIIHFHHGFIIHGIIIGHIIEGIHIHHHEGGIIIGGIIIIDGBIIIIICIDDEICGIFII=IIEHFDDHIIIIIII;DAGEBI?\n  @simulated.3\n  AGTCCTGTGAGCACCACCGGAATAGTACTGGAAATACTGACTTAATGTGCTCTTTGTGCTATCTGCGAGCCTACAACATGTTCATTTACAGTAAGTGTGC\n  $ head right.fq \n  @simulated.1\n  CCTATCTAATAATATACCTTATACTGGACTAGTGCCAATATTAAAATGAAGTGGGCGTAGTGTGTAATTTGATTGGGTGGAGGTGTGGCTTTGGCGTGCT\n  +\n  HHHHHIIHIHIHHIHHHIHHIIIFIHHHHIIIIGIGHIIIIEHIIIHHIIIBHHIIIHFIG?IIFIHGIGGIGDEBGIE?IHDEIIII?IIIGIC@IAIB\n  @simulated.2\n  ACGGGGAAACTCCACGTTGGCGCTCAAAGGGCGCGTTTATTGTTCTGTCAGCTGATCGTTTGGGTATTTAATGCCGCCGTGTTCGTCAAGAGGCCACTCT\n  +\n  HHHIIHHHHIHHHIHGFHIGHIEGGHGIFIIFHHHIIHIGCFEEIGIIIHIIECGFIDIDIEDABFGIIEFHIHAI\u003cIIIHAIEHIH\u003eICIHIGGIIIIG\n  @simulated.3\n  TGCTATTAGGTTCAGGCTCATTATCGGAAACAGGACCTAAAAACAACAAAATATTATTTTTCACTGCTTAAGAAAAAAAAATCACCTCCCACCTCCCATA\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fmason","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fseqan%2Fmason","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fmason/lists"}