{"id":17012360,"url":"https://github.com/sam-k/seq-quality-trimming","last_synced_at":"2025-04-19T23:54:20.023Z","repository":{"id":108348220,"uuid":"166301146","full_name":"sam-k/seq-quality-trimming","owner":"sam-k","description":"Trimming Sanger sequencing reads by quality","archived":false,"fork":false,"pushed_at":"2019-03-07T01:57:16.000Z","size":17,"stargazers_count":6,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-04-19T23:54:15.954Z","etag":null,"topics":["dna","genomics","metabarcoding","sequencing","ta-cloning"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sam-k.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-01-17T21:42:28.000Z","updated_at":"2024-11-15T16:17:34.000Z","dependencies_parsed_at":"2023-05-21T22:45:30.656Z","dependency_job_id":null,"html_url":"https://github.com/sam-k/seq-quality-trimming","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sam-k%2Fseq-quality-trimming","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sam-k%2Fseq-quality-trimming/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sam-k%2Fseq-quality-trimming/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sam-k%2Fseq-quality-trimming/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sam-k","download_url":"https://codeload.github.com/sam-k/seq-quality-trimming/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249830852,"owners_count":21331357,"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","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":["dna","genomics","metabarcoding","sequencing","ta-cloning"],"created_at":"2024-10-14T06:10:26.870Z","updated_at":"2025-04-19T23:54:20.003Z","avatar_url":"https://github.com/sam-k.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# seq-quality-trimming\nTrimming and merging reads from .ab1 Sanger sequencing files.\n\nPart of the [human diet quantification project](http://el.ladlab.org:8080/), which aims to establish a model for quantifying dietary components from DNA metabarcoding data.\n\n## Quality trimming\n- Isolate segment with the highest quality from the sequence, using Kadane's algorithm.\n- Trim low-quality ends of the sequence.\n\n## Merging reads\n- Align the forward/reverse PCR products using the Smith-Waterman algorithm for local alignment.\n- Merge the reads if the overlap is large enough.\n\n## BLAST\n- BLAST the merged sequence.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsam-k%2Fseq-quality-trimming","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsam-k%2Fseq-quality-trimming","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsam-k%2Fseq-quality-trimming/lists"}