{"id":23071289,"url":"https://github.com/clinical-genomics/microsalt","last_synced_at":"2025-08-15T14:32:16.597Z","repository":{"id":25842105,"uuid":"106690880","full_name":"Clinical-Genomics/microSALT","owner":"Clinical-Genomics","description":"Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.","archived":false,"fork":false,"pushed_at":"2024-12-16T04:08:20.000Z","size":1672,"stargazers_count":2,"open_issues_count":17,"forks_count":3,"subscribers_count":9,"default_branch":"master","last_synced_at":"2024-12-16T05:19:50.385Z","etag":null,"topics":["clinical","microbial","pipeline","resistance","typing"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Clinical-Genomics.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":".github/CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-10-12T12:38:03.000Z","updated_at":"2024-11-21T07:21:19.000Z","dependencies_parsed_at":"2023-01-14T03:32:02.939Z","dependency_job_id":"1f0fd4f6-7053-490d-b77c-991036eb926a","html_url":"https://github.com/Clinical-Genomics/microSALT","commit_stats":{"total_commits":999,"total_committers":25,"mean_commits":39.96,"dds":0.6646646646646647,"last_synced_commit":"a944d3f1660bc9c6db2cdecefbb2e755a51cf1db"},"previous_names":[],"tags_count":17,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2FmicroSALT","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2FmicroSALT/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2FmicroSALT/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2FmicroSALT/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Clinical-Genomics","download_url":"https://codeload.github.com/Clinical-Genomics/microSALT/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":229920920,"owners_count":18144863,"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":["clinical","microbial","pipeline","resistance","typing"],"created_at":"2024-12-16T07:13:23.657Z","updated_at":"2024-12-16T07:13:24.334Z","avatar_url":"https://github.com/Clinical-Genomics.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build status](https://github.com/clinical-genomics/microsalt/actions/workflows/run_tests.yml/badge.svg)](https://github.com/clinical-genomics/microsalt/actions/workflows/run_tests.yml)\n[![Coverage Status](https://coveralls.io/repos/github/Clinical-Genomics/microSALT/badge.svg?branch=master)](https://coveralls.io/github/Clinical-Genomics/microSALT?branch=master)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4026043.svg)](https://doi.org/10.5281/zenodo.4026043)\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://github.com/sylvinite/microSALT\"\u003e\n    \u003cimg width=\"1000\" height=\"250\" src=\"artwork/microsalt.jpg\"/\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n__Microbial Sequence Analysis and Loci-based Typing pipeline__\n\n_The microbial sequence analysis and loci-based typing pipeline (microSALT) is\nused to analyse microbial samples.  It produces a quality control of the\nsample, determines a sample's organism specific sequence type, and its\nresistance pattern. microSALT also provides a database storage solution and\nreport generation of these results._\n\n_microSALT uses a combination of python, sqLite and flask. Python is used for\nthe majority of functionality, the database is handled through sqLite and the\nfront-end is handled through flask. All analysis activity by microSALT requires\na SLURM cluster._\n\n## Quick installation\n\n1. `yes | bash \u003c(curl https://raw.githubusercontent.com/Clinical-Genomics/microSALT/master/install.sh)`\n2. `cp configExample.json $HOME/.microSALT/config.json`\n3. `vim $HOME/.microSALT/config.json`\n\n## Configuration\n\nCopy the configuration file to microSALTs hidden home directory, _or_ copy the\nconfiguration file anywhere and direct the envvar MICROSALT_CONFIG to it. See\nexample:\n\n`cp configExample.json $HOME/.microSALT/config.json`\n\n_or_\n\n```\ncp configExample.json /MY/FAV/FOLDER/config.json\nexport MICROSALT_CONFIG=/MY/FAV/FOLDER/config.json\n```\n\n__Then edit the fields to match your environment__.\n\n## Usage\n\n- `microSALT analyse` contains functions to start sbatch job(s) \u0026 produce\n  output to `folders['results']`. Afterwards the parsed results  are uploaded\n  to the SQL back-end and produce reports (HTML), which are then automatically\n  e-mailed to the user.\n- `microSALT utils` contains various functionality, including generating the\n  sample description json, manually adding new reference organisms and\n  re-generating reports.\n\n## Databases\n\n### MLST Definitions\n\nmicroSALT will automatically download \u0026 use the MLST definitions for any\norganism on [pubMLST](https://pubmlst.org/databases). Other definitions may be\nused, as long as they retain the same format.\n\n### Resistance genes\n\nmicroSALT will automatically download \u0026 use the resistance genes of [ResFinder](https://bitbucket.org/genomicepidemiology/resfinder).\nAny definitions will work, as long as they retain the same formatting.\n\n## Requirements\n\n### Hardware\n\n- A [SLURM](https://slurm.schedmd.com) enabled HPC system\n- A (clarity) LIMS server\n\n### Software\n\n- [Conda](https://conda.io)\n- Python 3.6\n- [SQLite](https://www.sqlite.org)\n\n## Contributing to this repo\n\nThis repository follows the Github flow approach to adding updates.\nFor more information, see https://guides.github.com/introduction/flow/\n\n## Credits\n\n- Isak Sylvin - Lead developer\n- Emma Sernstad - Accreditation ready reports\n- Tanja Normark - Various issues\n- Maya Brandi - Various issues\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclinical-genomics%2Fmicrosalt","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fclinical-genomics%2Fmicrosalt","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclinical-genomics%2Fmicrosalt/lists"}