{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"graphtyper","owner":"DecodeGenetics","isFork":false,"description":"Population-scale genotyping using pangenome graphs","allTopics":["bioinformatics","genetics","genotype","decode-genetics","graph","variants"],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":58,"starsCount":162,"forksCount":20,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-29T13:50:08.163Z"}},{"type":"Public","name":"Ratatosk","owner":"DecodeGenetics","isFork":false,"description":"Hybrid error correction of long reads using colored de Bruijn graphs","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":94,"forksCount":7,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-10T09:12:28.096Z"}},{"type":"Public","name":"popSTR","owner":"DecodeGenetics","isFork":false,"description":"PopSTR - A Population based microsatellite genotyper","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":5,"starsCount":31,"forksCount":9,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-23T05:01:05.990Z"}},{"type":"Public","name":"gnonadd","owner":"DecodeGenetics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-26T20:43:47.377Z"}},{"type":"Public","name":"proteomics_comparison","owner":"DecodeGenetics","isFork":false,"description":"Supplementary code for the article \"Large-scale plasma proteomics comparisons through genetics and disease associations\"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-16T10:27:49.143Z"}},{"type":"Public","name":"mDNM_analysisAndData","owner":"DecodeGenetics","isFork":false,"description":"Scripts for mDNM analysis and the data the analysis was run on.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-01T13:12:21.095Z"}},{"type":"Public","name":"NCOurd","owner":"DecodeGenetics","isFork":false,"description":"Modelling Length Distributions of NCO Events and Gene Conversion Tracts","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-16T14:37:29.678Z"}},{"type":"Public","name":"popvcf","owner":"DecodeGenetics","isFork":false,"description":"Lossless VCF compression","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":1,"starsCount":18,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-03-04T14:42:25.617Z"}},{"type":"Public","name":"LRcaller","owner":"DecodeGenetics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":2,"starsCount":16,"forksCount":3,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-01-10T12:04:20.140Z"}},{"type":"Public","name":"LRS_SV_sets","owner":"DecodeGenetics","isFork":false,"description":"VCF files of SVs using long-read sequencing (LRS).","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":1,"starsCount":21,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-12-17T16:23:54.750Z"}},{"type":"Public","name":"sv-merger","owner":"DecodeGenetics","isFork":true,"description":"Forms SV cliques using the CAST (Cluster Affinity Search Technique) algorithm.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":8,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-11-29T12:20:51.090Z"}},{"type":"Public","name":"COVID19_reconstruction_iceland","owner":"DecodeGenetics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-06-10T13:44:49.851Z"}},{"type":"Public","name":"graphtyper-pipelines","owner":"DecodeGenetics","isFork":false,"description":"Recommended Graphtyper pipelines","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":2,"starsCount":14,"forksCount":4,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-02-22T09:48:25.385Z"}},{"type":"Public","name":"SquiggleSV_samplerun","owner":"DecodeGenetics","isFork":false,"description":"Sample run with test data on the squigglesv branch of Nanopolish","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-02-03T13:29:16.854Z"}},{"type":"Public","name":"svimmer","owner":"DecodeGenetics","isFork":false,"description":"Structural variant merging tool","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":4,"starsCount":43,"forksCount":9,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-01-07T12:44:49.637Z"}},{"type":"Public","name":"read_haps","owner":"DecodeGenetics","isFork":false,"description":"Detects human contamination in bam files","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":16,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-09-10T15:26:35.465Z"}},{"type":"Public","name":"BamHash","owner":"DecodeGenetics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":6,"starsCount":36,"forksCount":8,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-08-13T06:58:21.780Z"}},{"type":"Public","name":"BamQC","owner":"DecodeGenetics","isFork":false,"description":"Quality control for BAM files","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-01-27T13:11:17.488Z"}},{"type":"Public","name":"nanopolish","owner":"DecodeGenetics","isFork":true,"description":"Signal-level algorithms for MinION data","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":160,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-12-10T12:44:46.512Z"}},{"type":"Public","name":"scrappie","owner":"DecodeGenetics","isFork":true,"description":"Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":26,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-11-22T14:49:39.826Z"}},{"type":"Public","name":"SViper","owner":"DecodeGenetics","isFork":true,"description":"Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":8,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-11-21T16:57:18.326Z"}},{"type":"Public","name":"Nanopolish_SVsquigglefilter","owner":"DecodeGenetics","isFork":false,"description":"Extension to nanopolish to compute alt-ref allele likelihood differences for suggested SVs using the squiggles of reads involved.","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-06-20T13:12:13.500Z"}},{"type":"Public","name":"bamLiftOver","owner":"DecodeGenetics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-12-13T11:16:56.787Z"}},{"type":"Public","name":"SeqAnHTS","owner":"DecodeGenetics","isFork":false,"description":"A SeqAn 2.1 fork that can use htslib","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-12-12T13:37:19.878Z"}},{"type":"Public","name":"bamShrink","owner":"DecodeGenetics","isFork":false,"description":"Filter for BAM-files","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":1,"starsCount":5,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-09-25T13:15:19.132Z"}},{"type":"Public","name":"chopBAI","owner":"DecodeGenetics","isFork":false,"description":"Chops a bam index file into pieces","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":1,"issueCount":1,"starsCount":5,"forksCount":1,"license":"GNU General Public License v2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-03-30T21:34:10.316Z"}}],"repositoryCount":26,"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"}