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    • The ARTIC field bioinformatics pipeline
      Python
      8912570Updated Jul 17, 2025Jul 17, 2025
    • Primalscheme3. Generation of highly multiplex primerschemes
      HTML
      61640Updated Jul 16, 2025Jul 16, 2025
    • Nextflow
      0310Updated Jul 16, 2025Jul 16, 2025
    • scylla

      Public
      single sample processing
      Python
      4860Updated Jul 2, 2025Jul 2, 2025
    • Generate a run sample sheet to input to amplicon-nf
      Nextflow
      0000Updated Jul 1, 2025Jul 1, 2025
    • artic-doc

      Public
      HTML
      0100Updated Jun 27, 2025Jun 27, 2025
    • Interactive workflow to run squirrel
      Nextflow
      1000Updated Jun 26, 2025Jun 26, 2025
    • website

      Public
      HTML
      6301Updated Jun 26, 2025Jun 26, 2025
    • ARTIC Epi2me compatible workflow and reporting
      Nextflow
      36311Updated Jun 23, 2025Jun 23, 2025
    • civet

      Public
      Cluster Investigation & Virus Epidemiology Tool
      Python
      1450320Updated Jun 17, 2025Jun 17, 2025
    • Python
      4300Updated Apr 16, 2025Apr 16, 2025
    • rampart

      Public
      Read Assignment, Mapping, and Phylogenetic Analysis in Real Time
      JavaScript
      34812817Updated Mar 11, 2025Mar 11, 2025
    • Nextflow wrapper for RAMPART
      Nextflow
      0000Updated Mar 11, 2025Mar 11, 2025
    • phylofunk

      Public
      Java
      0200Updated Mar 8, 2025Mar 8, 2025
    • aubergine

      Public
      Nextflow
      0000Updated Mar 7, 2025Mar 7, 2025
    • Dockerfile
      1000Updated Mar 5, 2025Mar 5, 2025
    • A repository of information and resources about viruses in the genus Ebolavirus
      1111Updated Jan 31, 2025Jan 31, 2025
    • bed2idt

      Public
      Convert bedfiles to IDT custom spreadsheets
      Python
      1100Updated Dec 20, 2024Dec 20, 2024
    • Collection of Scripts for the OT2 for pooling primers
      Python
      0100Updated Dec 20, 2024Dec 20, 2024
    • HTML
      0400Updated Dec 20, 2024Dec 20, 2024
    • artic-rsv

      Public
      Nextflow
      3550Updated Aug 2, 2024Aug 2, 2024
    • Repository for realtime sequencing of measles virus using the MinION
      5120Updated Sep 14, 2023Sep 14, 2023
    • 0100Updated Sep 14, 2023Sep 14, 2023
    • 0100Updated Sep 14, 2023Sep 14, 2023
    • A RAMPART protocol and environment for sequencing Ebola viruses
      1100Updated Sep 14, 2023Sep 14, 2023
    • Primer schemes for real-time genome epidemiology
      Python
      422920Updated Jun 14, 2023Jun 14, 2023
    • ARTIC nanopore protocol for nCoV2019 novel coronavirus
      Python
      164170442Updated Mar 22, 2023Mar 22, 2023
    • HTML
      0000Updated Oct 25, 2022Oct 25, 2022
    • polecat

      Public
      Python
      1910Updated Feb 27, 2021Feb 27, 2021
    • Porechop

      Public
      adapter trimmer for Oxford Nanopore reads
      C++
      132701Updated Nov 15, 2020Nov 15, 2020