{"id":22621081,"url":"https://github.com/pdimens/shortle","last_synced_at":"2026-07-28T12:32:11.428Z","repository":{"id":154347865,"uuid":"589805599","full_name":"pdimens/shortle","owner":"pdimens","description":"A Pretty Ok Short-Read Assembly Workflow","archived":false,"fork":false,"pushed_at":"2023-01-18T21:32:16.000Z","size":21,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-10-10T19:35:47.957Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/pdimens.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-01-17T01:16:17.000Z","updated_at":"2023-01-17T01:17:30.000Z","dependencies_parsed_at":"2024-06-12T21:16:40.834Z","dependency_job_id":null,"html_url":"https://github.com/pdimens/shortle","commit_stats":{"total_commits":10,"total_committers":1,"mean_commits":10.0,"dds":0.0,"last_synced_commit":"506f4c6dc75afb282db8c35d61b1b960d4730651"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/pdimens/shortle","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fshortle","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fshortle/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fshortle/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fshortle/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pdimens","download_url":"https://codeload.github.com/pdimens/shortle/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fshortle/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35992000,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-07-20T02:08:10.276Z","status":"online","status_checked_at":"2026-07-28T02:00:06.341Z","response_time":109,"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":"2024-12-08T22:17:38.906Z","updated_at":"2026-07-28T12:32:11.363Z","avatar_url":"https://github.com/pdimens.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# shortle\nA Pretty Ok Short-Read Assembly Workflow\n\n\n## How to use me\n1. You'll need some reads\n- Preferably paired-end\n- Preferably one file each for foward and reverse reads\n\n2. You'll need conda/mamba (recommended: mamba) and to install the main conda environment, provided by `shortle.yaml` in the main directory of this repository. The remaining software is provided in `workflow/envs/redundans.yaml`, which will be used by Snakemake, so you don't need to worry about it.\n```bash\nconda env create -f shortle.yaml\n```\nThis command will create an environment called `shortle`. Activate it with:\n```bash\nconda activate shortle\n```\n\n3. You'll need to modify the first few lines that specify the forward/reverse read information in `Snakefile` to match your data. You'll also want to modify any parameters for `sparseassembler`, `dbg2olc` and `abyss` as you see fit. The values there are from previous projects and reflect _those_ data. Adjust your `k` paramters accordingly (or wing it).\n\n4. You'll need to run it once with the specific command to end it prematurely (at the purge_haplotigs stage):\n```bash\nsnakemake -j 20 --use-conda purge_haplotigs/mapped2.bam.gencov\n```\nwhere `j` is how many cores you are willing to reserve for the Snakemake workflow.\n\n5. Inspect `purge_haplotigs/mapped2.bam.histogram.png` to figure out your cutoffs as described [here](https://bitbucket.org/mroachawri/purge_haplotigs/src/master/): ![purge haplotigs histogram](https://bitbucket.org/repo/Ej8Mz7/images/1039246939-coverage_histogram.png)\n\n6. Modify `rule purge_haplotigs_suspects` to match your chosen cutoffs and rerun the entire workflow:\n```bash\nsnakemake -j 20 --use-conda\n```\n\n7. Your resulting assembly will be in `polish_2`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdimens%2Fshortle","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpdimens%2Fshortle","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdimens%2Fshortle/lists"}