{"payload":{"pageCount":4,"repositories":[{"type":"Public","name":"fluviewer-nf","owner":"BCCDC-PHL","isFork":false,"description":"Nextflow pipeline for influenza A whole genome sequence analysis","allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":1,"issueCount":4,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-09T18:09:07.168Z"}},{"type":"Public","name":"tbprofiler-nf","owner":"BCCDC-PHL","isFork":false,"description":"Nextflow Wrapper for TBProfiler","allTopics":["bioinformatics-pipeline","microbial-genomics","tuberculosis-classification"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":2,"starsCount":4,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-03T10:29:08.100Z"}},{"type":"Public","name":"cpo-results-collector","owner":"BCCDC-PHL","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-02T19:23:14.334Z"}},{"type":"Public","name":"demultiplex-nanopore","owner":"BCCDC-PHL","isFork":false,"description":"Demultiplex nanopore reads and combine into a single file per sample","allTopics":["microbial-genomics","nanopore-sequencing"],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-31T21:37:38.198Z"}},{"type":"Public","name":"WasteFlow","owner":"BCCDC-PHL","isFork":false,"description":"Nextflow pipeline for pathogen surveillance in wastewater","allTopics":["nextflow","surveillance","wastewater","freyja","sars-cov-2","microbes"],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-30T23:54:28.835Z"}},{"type":"Public","name":"auto-cpo","owner":"BCCDC-PHL","isFork":false,"description":"Automation of Genomic Analyses for Carbapenemase-Producing Organisms (CPOs)","allTopics":["automation","microbial-genomics"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":5,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-30T23:10:37.686Z"}},{"type":"Public","name":"dehost-and-verify-illumina","owner":"BCCDC-PHL","isFork":false,"description":"Remove host reads from a microbial pathogen sequence dataset by aligning against a reference genome. Verify that the reads were removed using Kraken2/Bracken","allTopics":["quality-control","microbial-genomics"],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":3,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-23T20:05:18.791Z"}},{"type":"Public","name":"symlink-seqs","owner":"BCCDC-PHL","isFork":false,"description":"Create fastq symlinks for selected samples in sequencer output directories based on several criteria","allTopics":["next-generation-sequencing","data-management","illumina-sequencing","symlinks-manager"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-23T20:02:20.172Z"}},{"type":"Public","name":"kma-cgmlst","owner":"BCCDC-PHL","isFork":false,"description":"A cgMLST pipeline based on the KMA aligner","allTopics":["bioinformatics-pipeline","microbial-genomics","cgmlst"],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":3,"starsCount":3,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-22T21:48:59.196Z"}},{"type":"Public","name":"FluViewer","owner":"BCCDC-PHL","isFork":true,"description":"Tool for generating influenza A virus genome sequences from FASTQ data","allTopics":["microbial-genomics","consensus-sequence","influenza-virus"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":3,"starsCount":4,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-22T20:15:31.792Z"}},{"type":"Public","name":"nfvibrio","owner":"BCCDC-PHL","isFork":true,"description":"Nextflow pipeline to run metagenomic sequence analysis of Vibrio Parahaemolyticus, based on nf-core template, by John Palmer & Zohaib Anwar","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-22T16:01:17.655Z"}},{"type":"Public","name":"auto-flu","owner":"BCCDC-PHL","isFork":false,"description":"Automated analysis of flu sequence data using BCCDC-PHL/fluviewer-nf","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-18T18:12:29.331Z"}},{"type":"Public","name":"auspice","owner":"BCCDC-PHL","isFork":true,"description":"Web app for visualizing pathogen evolution","allTopics":[],"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":161,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-16T21:20:21.658Z"}},{"type":"Public","name":"noro-phylo-nf","owner":"BCCDC-PHL","isFork":false,"description":"Pipeline for performing multiple sequence alignment and phylogenetic tree reconstruction on norovirus sequence data. ","allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-16T18:29:47.137Z"}},{"type":"Public","name":"routine-sequence-qc-site","owner":"BCCDC-PHL","isFork":false,"description":"A site for displaying routine sequence QC data","allTopics":["quality-control","clojurescript","next-generation-sequencing","microbial-genomics"],"primaryLanguage":{"name":"Clojure","color":"#db5855"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-12T00:24:04.831Z"}},{"type":"Public","name":"auto-illumina-run-qc-check","owner":"BCCDC-PHL","isFork":false,"description":"Automated Primary Sequence QC Checks for Illumina Sequencing Runs","allTopics":["quality-control","next-generation-sequencing","laboratory-automation"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-11T22:55:27.286Z"}},{"type":"Public","name":"noro-typing-nf","owner":"BCCDC-PHL","isFork":false,"description":"Norovirus metagenomics Nextflow pipeline","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-09T20:47:32.998Z"}},{"type":"Public","name":"amplicon-consensus","owner":"BCCDC-PHL","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-05T20:28:27.901Z"}},{"type":"Public","name":"alignment-variants","owner":"BCCDC-PHL","isFork":false,"description":"Pipeline to perform alignment & variant calling on whole-genome sequence data","allTopics":["microbial-genomics","variant-calling","read-mapping"],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-05T17:47:57.254Z"}},{"type":"Public","name":"plasmid-screen","owner":"BCCDC-PHL","isFork":false,"description":"Screen plasmids for carbapenemase resistance genes, and classify using MOB Suite","allTopics":["bioinformatics-pipeline","antibiotic-resistance","plasmids","genomic-epidemiology"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":4,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-21T16:45:34.244Z"}},{"type":"Public","name":"auto-hcv","owner":"BCCDC-PHL","isFork":false,"description":"Automated genomic analysis of HCV sequence data","allTopics":["automation","microbial-genomics"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-14T20:05:31.692Z"}},{"type":"Public","name":"16s-nf","owner":"BCCDC-PHL","isFork":false,"description":"Prepare a report for taxonomic assignment based on 16S rRNA sequences, using BLAST.","allTopics":["microbial-genomics","taxonomic-classification","16s-rrna"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-14T18:36:18.475Z"}},{"type":"Public","name":"illumina-uploader","owner":"BCCDC-PHL","isFork":false,"description":"Watch for new files in Illumina sequencer and upload to remote server","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":6,"starsCount":2,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-10T17:53:15.332Z"}},{"type":"Public","name":"routine-assembly","owner":"BCCDC-PHL","isFork":false,"description":"Pipeline for performing routine genome assembly","allTopics":["bioinformatics-pipeline","genome-annotation","genome-assembly"],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-07T23:05:20.601Z"}},{"type":"Public","name":"genomics-services-monitor","owner":"BCCDC-PHL","isFork":false,"description":"Tool for Monitoring Genomics Services","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-06T00:15:40.504Z"}},{"type":"Public","name":"auto-tb-amr-amplicon","owner":"BCCDC-PHL","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":"2024-05-30T22:44:14.264Z"}},{"type":"Public","name":"noro-meta-nf","owner":"BCCDC-PHL","isFork":false,"description":"Nextflow pipeline for classification and quantification of metagenomic samples.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-27T17:37:33.352Z"}},{"type":"Public","name":"mpxv-qc","owner":"BCCDC-PHL","isFork":false,"description":"Companion pipeline to perform quality control for BCCDC-PHL/mpxv-artic-nf","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-17T20:47:23.880Z"}},{"type":"Public","name":"cpo-qc-site","owner":"BCCDC-PHL","isFork":false,"description":"Website for display of Genomics QC Data for Carbapenemase-Producing Organisms (CPOs)","allTopics":["quality-control","microbial-genomics"],"primaryLanguage":{"name":"Clojure","color":"#db5855"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-17T18:57:03.798Z"}},{"type":"Public","name":"flu-helper-scripts","owner":"BCCDC-PHL","isFork":false,"description":"A set of scripts for working with Influenza data","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-14T21:09:34.868Z"}}],"repositoryCount":118,"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":"BCCDC-PHL repositories"}