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    14 repositories

    • taxtriage

      Public
      TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.
      taxonomymetagenomicsclassificationmultiqctriage
      Python
      •
      MIT License
      •4•21•7•0•Updated Oct 4, 2024Oct 4, 2024

    • TgIF

      Public
      Trans-gene Insertion Finder
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

    • mytax

      Public
      mytax is a tool for building custom taxonomies, useful for nucleotide sequence classification
      JavaScript
      •
      GNU Affero General Public License v3.0
      •2•11•0•1•Updated Aug 22, 2024Aug 22, 2024

    • Basestack

      Public
      Basestack is a platform for rapid and real time analysis of NGS data. It provides a executable application that connects standard bionformatics tools to a user interface. It is usable on all major Linux distributions, Mac OS, and Windows 10 or later
      linuxdockermacguiinterfacewindows-10suiteconsensus-generation
      JavaScript
      •
      GNU General Public License v3.0
      •1•26•3•1•Updated Jul 23, 2024Jul 23, 2024

    • ONT-DART

      Public
      Vue
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 14, 2024Jun 14, 2024

    • datasets

      Public
      General repository for example datasets
      HTML
      •0•0•0•0•Updated May 14, 2024May 14, 2024

    • omics_workshop

      Public
      This is the central repository for data and example commands for bioinformatics workshop used for JHU-APL faculty and participant use
      HTML
      •0•0•0•0•Updated Apr 29, 2024Apr 29, 2024

    • AGAVE

      Public
      Automated Genomics Application for Variant Exploration (AGAVE)
      variant-analysisvirologyvue
      Vue
      •
      GNU General Public License v3.0
      •0•2•3•0•Updated Feb 14, 2024Feb 14, 2024

    • GE-Workshop-Sandbox

      Public
      Dockerfile
      •0•0•0•0•Updated Sep 18, 2023Sep 18, 2023

    • mytax_marine

      Public
      Shell
      •0•0•0•0•Updated May 12, 2023May 12, 2023

    • mytax_marine_old

      Public
      mytax with added information on marine organisms, including common names, pictures, and population distribution
      Vue
      •
      GNU Affero General Public License v3.0
      •2•0•0•0•Updated Sep 14, 2022Sep 14, 2022

    • pathogenesis-gene-ontology

      Public
      An ontology for the functional annotation of genes and gene products involved in pathogenesis
      bioinformaticsontology
      C++
      •1•1•36•0•Updated Mar 8, 2022Mar 8, 2022

    • basestack_consensus

      Public
      This repository is a Dockerized pipeline for creating consensus viral genomes from Oxford Nanopore data. This pipeline leverages the ARTIC Network bioinformatics pipeline and couples many annotation and reporting tools, resulting in an automatically generated PDF report. The pipeline is built to be deployed in the Basestack platform (https://git…
      Shell
      •
      GNU General Public License v3.0
      •2•2•16•1•Updated Sep 1, 2021Sep 1, 2021

    • nCovIllumina

      Public
      Python
      •2•0•1•0•Updated Feb 20, 2021Feb 20, 2021