{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"MultiLab-POD-LOD-ICC","owner":"CFSAN-Biostatistics","isFork":false,"description":"This is a Shiny app for interlaboratory microbiological method validation studies.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T15:46:15.149Z"}},{"type":"Public","name":"CSP2","owner":"CFSAN-Biostatistics","isFork":false,"description":"A Nextflow pipeline for fast and accurate SNP distance estimation from WGS read data or genome assemblies","allTopics":[],"primaryLanguage":{"name":"Roff","color":"#ecdebe"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-23T23:15:11.628Z"}},{"type":"Public","name":"RIPS","owner":"CFSAN-Biostatistics","isFork":false,"description":"RIPS-Rapid Intuitive Pathogen Surveillance ","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-25T14:29:55.397Z"}},{"type":"Public","name":"One_Health_Enteric_Package","owner":"CFSAN-Biostatistics","isFork":false,"description":"One Health-compatible metadata package for genomic surveillance of enteric microbes","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":1,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-21T15:58:13.082Z"}},{"type":"Public","name":"cronology","owner":"CFSAN-Biostatistics","isFork":false,"description":"cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.","allTopics":["nextflow","mlst","subtyping","nextflow-pipelines","cronobacter","ncbi-pathoges"],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-14T15:59:11.152Z"}},{"type":"Public","name":"porerefiner","owner":"CFSAN-Biostatistics","isFork":false,"description":"A tool for managing your pores","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":10,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-23T04:33:15.853Z"}},{"type":"Public template","name":"mlst-hash-template","owner":"CFSAN-Biostatistics","isFork":true,"description":"This is a template for any new hash-based MLST database","allTopics":[],"primaryLanguage":{"name":"Perl","color":"#0298c3"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-23T04:20:41.329Z"}},{"type":"Public","name":"microrunqc-wdl","owner":"CFSAN-Biostatistics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"WDL","color":"#42f1f4"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":2,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-10T23:40:15.300Z"}},{"type":"Public","name":"bettercallsal","owner":"CFSAN-Biostatistics","isFork":false,"description":"Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.","allTopics":["nextflow","metagenomics","salmonella","nextflow-pipelines","ncbi-pathogens","quasi-metagenomics"],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":7,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-05T16:42:42.352Z"}},{"type":"Public","name":"WW-SC2-variant-estimations","owner":"CFSAN-Biostatistics","isFork":false,"description":"","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-08T18:05:52.197Z"}},{"type":"Public","name":"C-WAP","owner":"CFSAN-Biostatistics","isFork":false,"description":"SC2 variant detection and composition pipeline","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":3,"starsCount":16,"forksCount":8,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-14T01:33:50.704Z"}},{"type":"Public","name":"shigatyper","owner":"CFSAN-Biostatistics","isFork":false,"description":"CFSAN Shigella Typing Pipeline","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":14,"forksCount":6,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-06T00:00:57.455Z"}},{"type":"Public","name":"vcftoolz","owner":"CFSAN-Biostatistics","isFork":false,"description":"Tools for working with Variant Call Format files.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":7,"starsCount":8,"forksCount":3,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-02T03:27:31.436Z"}},{"type":"Public","name":"Freyja","owner":"CFSAN-Biostatistics","isFork":true,"description":"Depth-weighted De-Mixing ","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":29,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-22T03:06:38.662Z"}},{"type":"Public","name":"snp-pipeline","owner":"CFSAN-Biostatistics","isFork":false,"description":"SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":4,"starsCount":55,"forksCount":31,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-05T03:45:41.850Z"}},{"type":"Public","name":"torchbase","owner":"CFSAN-Biostatistics","isFork":true,"description":"Python framework for microbial typing by reference","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-17T03:34:56.864Z"}},{"type":"Public","name":"wdl-commons","owner":"CFSAN-Biostatistics","isFork":false,"description":"Common WDL task components for bioinformatics workflows.","allTopics":[],"primaryLanguage":{"name":"WDL","color":"#42f1f4"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-18T04:44:25.889Z"}},{"type":"Public","name":"refchooser","owner":"CFSAN-Biostatistics","isFork":false,"description":"Tools to help choose a reference from a list of assemblies.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":1,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-26T19:45:49.106Z"}},{"type":"Public","name":"SeroTools","owner":"CFSAN-Biostatistics","isFork":false,"description":"A toolkit and repository for the White-Kauffmann-Le Minor scheme for Salmonella serotyping.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":2,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-26T19:45:48.947Z"}},{"type":"Public","name":"kyos","owner":"CFSAN-Biostatistics","isFork":false,"description":"Tools for haploid variant calling with Deep Neural Networks.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":1,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-26T19:45:47.489Z"}},{"type":"Public","name":"jobrunner","owner":"CFSAN-Biostatistics","isFork":false,"description":"An abstraction layer to run jobs on HPC clusters using Grid Engine, Torque, or locally.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":2,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-26T19:45:47.373Z"}},{"type":"Public","name":"qarrayrun","owner":"CFSAN-Biostatistics","isFork":false,"description":"A helper tool for running array jobs on an HPC computational node.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":1,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-26T19:45:46.978Z"}},{"type":"Public","name":"fastatools","owner":"CFSAN-Biostatistics","isFork":false,"description":"Tools for working with fasta files.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":1,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-26T19:45:44.776Z"}},{"type":"Public","name":"snp-mutator","owner":"CFSAN-Biostatistics","isFork":false,"description":"Generate mutated sequence files from a reference genome.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":10,"forksCount":4,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-26T19:44:01.282Z"}},{"type":"Public","name":"RabbitTClust","owner":"CFSAN-Biostatistics","isFork":true,"description":"RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":3,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-13T14:49:53.042Z"}},{"type":"Public","name":"table-ops","owner":"CFSAN-Biostatistics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-28T05:30:46.157Z"}},{"type":"Public","name":"ww_simulations","owner":"CFSAN-Biostatistics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":2,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-09-28T21:11:04.987Z"}},{"type":"Public","name":"galaxy-worflows","owner":"CFSAN-Biostatistics","isFork":false,"description":"Galaxy workflows that are published by CFSAN","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-12-09T23:10:27.062Z"}},{"type":"Public","name":"amrfinder-galaxy","owner":"CFSAN-Biostatistics","isFork":false,"description":"amrfinder-galaxy","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-11-09T01:22:36.787Z"}},{"type":"Public","name":"alphafold2","owner":"CFSAN-Biostatistics","isFork":true,"description":"To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":254,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-09-11T14:13:20.677Z"}}],"repositoryCount":45,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"Repositories"}