{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"depletion","owner":"sequana","isFork":false,"description":"Deplete Fastq files from human or other content","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":1,"starsCount":1,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-22T08:13:22.474Z"}},{"type":"Public","name":"fastqc","owner":"sequana","isFork":false,"description":"sequana pipeline to perform parallel fastqc and summarize results with multiqc plot","topicNames":["snakemake","ngs","fastqc","sequana"],"topicsNotShown":0,"allTopics":["snakemake","ngs","fastqc","sequana"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":7,"issueCount":0,"starsCount":3,"forksCount":3,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-21T06:58:40.909Z"}},{"type":"Public","name":"sequana_pipetools","owner":"sequana","isFork":false,"description":"A set of tools to help building or using sequana pipelines","topicNames":["ngs","sequana"],"topicsNotShown":0,"allTopics":["ngs","sequana"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":2,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-05T19:33:43.222Z"}},{"type":"Public","name":"bioconvert","owner":"sequana","isFork":false,"description":"convert files from one format to another using bioconvert","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":6,"issueCount":0,"starsCount":1,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-03T16:07:11.843Z"}},{"type":"Public","name":"revcomp","owner":"sequana","isFork":false,"description":"A simple utility to convert a bunch of input fastq files into their reverse complement","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":5,"issueCount":0,"starsCount":0,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-03T16:03:04.238Z"}},{"type":"Public","name":"quality_control","owner":"sequana","isFork":false,"description":"A quality control pipeline for illumina data set. This pipeline removes contaminants (e.g. Phix), performs fastqc, adapter cleaning and trimming and checks for contaminants","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":5,"issueCount":0,"starsCount":0,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-03T15:56:28.085Z"}},{"type":"Public","name":"denovo","owner":"sequana","isFork":false,"description":"Denovo Assembly from FASTQ files","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":0,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-25T14:27:16.328Z"}},{"type":"Public","name":"webapp_samplesheet","owner":"sequana","isFork":false,"description":"test st","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-20T10:18:54.429Z"}},{"type":"Public","name":"sequana","owner":"sequana","isFork":false,"description":"Sequana: a set of Snakemake NGS pipelines","topicNames":["coverage","rna-seq","snakemake","taxonomy","ngs","pacbio","variant-calling","de-novo","sequanix"],"topicsNotShown":0,"allTopics":["coverage","rna-seq","snakemake","taxonomy","ngs","pacbio","variant-calling","de-novo","sequanix"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":9,"starsCount":140,"forksCount":27,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-18T15:24:00.477Z"}},{"type":"Public","name":"GNFish","owner":"sequana","isFork":true,"description":"Suite of Python programs for Gene extraction and Phylogentic Inference","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":2,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-18T09:05:57.823Z"}},{"type":"Public","name":"sequana.github.io","owner":"sequana","isFork":false,"description":"resource for the website","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-10T17:15:04.099Z"}},{"type":"Public","name":"rnaseq","owner":"sequana","isFork":false,"description":"RNA-seq, QC and differential analysis pipeline","topicNames":["workflow","rna-seq","pipeline","ngs","differential-analysis","sequana"],"topicsNotShown":0,"allTopics":["workflow","rna-seq","pipeline","ngs","differential-analysis","sequana"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":5,"starsCount":17,"forksCount":4,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-22T21:15:47.123Z"}},{"type":"Public","name":"webapp_rnadiff","owner":"sequana","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-21T14:18:39.834Z"}},{"type":"Public","name":"sequanix","owner":"sequana","isFork":false,"description":"Sequanix is a graphical user interface (GUI) that can be used to run Snakemake workflows.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":4,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-20T09:00:46.091Z"}},{"type":"Public","name":"mapper","owner":"sequana","isFork":false,"description":"Pipeline to map a set of FastQ files","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":5,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-07T21:23:04.829Z"}},{"type":"Public","name":"sequana-wrappers","owner":"sequana","isFork":false,"description":"The Sequana Wrapper Repository is a collection of reusable wrappers used in Sequana Pipelines.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"CAP CDS","color":"#0092d1"},"pullRequestCount":0,"issueCount":9,"starsCount":0,"forksCount":3,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-06T19:06:01.322Z"}},{"type":"Public","name":"variant_calling","owner":"sequana","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":0,"forksCount":3,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-31T08:45:40.959Z"}},{"type":"Public","name":"versionix","owner":"sequana","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":3,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-16T09:54:42.040Z"}},{"type":"Public","name":"demultiplex","owner":"sequana","isFork":false,"description":"Sequana demultiplexing pipeline ","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":3,"forksCount":3,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-29T13:48:30.362Z"}},{"type":"Public","name":"lora","owner":"sequana","isFork":false,"description":"Run assembler (Canu, flye, hifiasm) on a set of long read files","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":5,"starsCount":2,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-20T14:46:05.357Z"}},{"type":"Public","name":"downsampling","owner":"sequana","isFork":false,"description":"down sample NGS data","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-20T12:43:58.215Z"}},{"type":"Public","name":"nanomerge","owner":"sequana","isFork":false,"description":"Pipeline utility to perform merge of barcoded nanopore runs","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-20T09:19:18.598Z"}},{"type":"Public","name":"laa","owner":"sequana","isFork":false,"description":"Pacbio amplicon, sequana, phylogeny, variant","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-19T11:32:50.141Z"}},{"type":"Public","name":"resources","owner":"sequana","isFork":false,"description":"Set of data and resources","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-06T07:54:21.311Z"}},{"type":"Public","name":"ribofinder","owner":"sequana","isFork":false,"description":"Workflow to find ribosomal feature in set of FastQ files","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-05T09:50:03.158Z"}},{"type":"Public","name":"sequana_pipeline_template","owner":"sequana","isFork":false,"description":"a cookiecutter sequana pipeline template","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-16T21:05:52.151Z"}},{"type":"Public","name":"pacbio_qc","owner":"sequana","isFork":false,"description":"QC on pacbio data ","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-07T13:12:18.551Z"}},{"type":"Public","name":"multicov","owner":"sequana","isFork":false,"description":"Snakemake pipeline wrapping sequana_coverage to analyse several samples at the same time","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":2,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-23T21:27:33.601Z"}},{"type":"Public","name":"circlator","owner":"sequana","isFork":true,"description":"A tool to circularize genome assemblies","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":56,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-24T15:29:02.958Z"}},{"type":"Public","name":"MergeGI","owner":"sequana","isFork":false,"description":"MergeGI provides a single command line to merge and select barcoded raw data from MGI sequencing runs into a set of FastQ files ready for subsequent bioinformatics analysis.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":3,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-10T10:06:32.087Z"}}],"repositoryCount":37,"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"}