{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"CoVpipe2","owner":"rki-mf1","isFork":false,"description":"SARS-CoV-2 genome reconstruction for Illumina data in Nextflow","allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":11,"starsCount":2,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-12T13:05:03.796Z"}},{"type":"Public","name":"cievad","owner":"rki-mf1","isFork":false,"description":"A tool suite for a simple, streamlined and rapid evaluation of variant callsets","allTopics":["benchmarking","bioinformatics","snps","genomics","nextflow","ngs","variant-calling","oxford-nanopore","indels"],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":5,"starsCount":1,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-10T11:35:29.851Z"}},{"type":"Public","name":"clean","owner":"rki-mf1","isFork":false,"description":"A nextflow pipeline for decontamination of short reads, long reads and contigs ","allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":1,"issueCount":11,"starsCount":24,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-10T08:54:38.007Z"}},{"type":"Public","name":"modules","owner":"rki-mf1","isFork":true,"description":"Repository to host tool-specific module files for the Nextflow DSL2 community!","allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":645,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-03T13:36:42.981Z"}},{"type":"Public","name":"PanAdapt","owner":"rki-mf1","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":2,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-25T10:08:14.926Z"}},{"type":"Public","name":"2024-Workshop-Namibia","owner":"rki-mf1","isFork":true,"description":"Practical introduction to long-read bioinformatics on the flu virus .","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":9,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-15T10:15:34.349Z"}},{"type":"Public","name":"amplisim","owner":"rki-mf1","isFork":false,"description":"Plain simple amplicon sequence simulator for in-silico genomic sequencing assays","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":7,"starsCount":2,"forksCount":0,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-07T14:47:33.805Z"}},{"type":"Public","name":"workshop-nanopore-bioinformatics","owner":"rki-mf1","isFork":true,"description":"Main resource for practical introductions to long-read bioinformatics.","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":13,"starsCount":1,"forksCount":9,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-07T10:14:51.018Z"}},{"type":"Public","name":"VLQ-nf","owner":"rki-mf1","isFork":false,"description":"Estimate SC2 lineage abundances from wastewater samples","allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":1,"issueCount":1,"starsCount":2,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-23T09:47:23.264Z"}},{"type":"Public","name":"update-varvamp-bed","owner":"rki-mf1","isFork":false,"description":"to update the primer bed positions from varvamp results based on given reference","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-14T12:42:09.416Z"}},{"type":"Public","name":"FluPipe","owner":"rki-mf1","isFork":false,"description":"Influenza genome reconstruction","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":3,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-19T12:51:27.385Z"}},{"type":"Public","name":"sc2-mutation-frequency-calculator","owner":"rki-mf1","isFork":false,"description":"Python tool to calculate characteristic and signature mutations based on mutation profiles for a certain timeframe.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-06T02:54:29.626Z"}},{"type":"Public","name":"MpoxRadar","owner":"rki-mf1","isFork":false,"description":"MpoxRadar frontend codebase: an interactive dashboard for genomic surveillance of MPXV.","allTopics":["dashboard","frontend","hpi","rki","genomic-surveillance","mpox"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":2,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-02T23:35:50.189Z"}},{"type":"Public","name":"covsonar","owner":"rki-mf1","isFork":false,"description":"A database-driven system for handling genomic sequences of SARS-CoV-2 and screening genomic profiles.","allTopics":["database","sars-cov-2","covsonar","covsonar2","genomic-profiles","bioinformatics"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":6,"starsCount":6,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-30T14:59:06.170Z"}},{"type":"Public","name":"2023-Workshop-Madagascar-IGS","owner":"rki-mf1","isFork":true,"description":"A practical introduction to short-read bioinformatics for bacterial genome reconstruction in the context of the Madagascar IGS workshop.ct.","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":9,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-12T10:53:52.901Z"}},{"type":"Public","name":"2023-GHPP-SGS-Nanopore-Metagenomics","owner":"rki-mf1","isFork":true,"description":"A practical introduction to long-read metagenomics in the context of the 2023 GHPP \"Strengthening Genomic Surveillance\" workshop..","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":4,"starsCount":2,"forksCount":9,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-27T19:44:58.348Z"}},{"type":"Public","name":"MpoxSonar","owner":"rki-mf1","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-27T12:03:48.505Z"}},{"type":"Public","name":"2023-SC2-Data-Science","owner":"rki-mf1","isFork":true,"description":"Material for the SARS-CoV-2 data science course at FU Berlin.","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":9,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-21T18:00:18.386Z"}},{"type":"Public","name":"2023-NGS-Summer-School","owner":"rki-mf1","isFork":true,"description":"NGS Summer School about Nanopore long-read bioinformatics and bacteria genome assembly.","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":9,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-30T08:56:11.588Z"}},{"type":"Public","name":"2023-Workshop-MISSIoN-Nanopore","owner":"rki-mf1","isFork":false,"description":"A practical introduction to long-read bioinformatics for bacterial genome reconstruction in the context of the Kenya MISSIoN project.","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":9,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-22T14:04:13.901Z"}},{"type":"Public","name":"Find_Giardia_Primer_Regions","owner":"rki-mf1","isFork":false,"description":"Snakemake pipeline to find potential giardia primer regions","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-20T09:54:07.999Z"}},{"type":"Public","name":"CoverageAnomalyScanner","owner":"rki-mf1","isFork":false,"description":"Application to find local anomalies in read coverage and to predict putative SV events","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":2,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-02T14:35:07.229Z"}},{"type":"Public","name":"LCS","owner":"rki-mf1","isFork":true,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-30T12:49:38.387Z"}},{"type":"Public","name":"vocal","owner":"rki-mf1","isFork":false,"description":"Vocal is a simple Variants Of Concern ALert system script. Doc https://rki-mf1.github.io/vocal-doc/","allTopics":["vocal","variant-detection","sars-cov-2","early-warning-system","integrated-molecular-surveillance"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":5,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-01T14:50:34.771Z"}},{"type":"Public","name":"president","owner":"rki-mf1","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":2,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-22T15:58:42.265Z"}},{"type":"Public","name":"breakfast","owner":"rki-mf1","isFork":false,"description":"breakfast is a simple and fast tool for clustering SARS-CoV-2 genomes using precalculated sequence features (e.g. nucleotide substitutions).","allTopics":["bioinformatics","clustering"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":6,"starsCount":10,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-10-04T11:29:15.366Z"}},{"type":"Public","name":"rki-mf1.github.io","owner":"rki-mf1","isFork":false,"description":"RKI Bioinformatics Research team page","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-04-04T08:35:25.527Z"}},{"type":"Public","name":"rubyscholar","owner":"rki-mf1","isFork":true,"description":"Scrape Google Scholar Profile into a custom HTML using Ruby (Nokogiri)","allTopics":[],"primaryLanguage":{"name":"Ruby","color":"#701516"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":5,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-10-24T18:35:16.327Z"}}],"repositoryCount":28,"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"}