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    45 repositories

    • artic-doc

      Public
      HTML
      •
      Other
      •3•0•3•0•Updated Dec 22, 2025Dec 22, 2025

    • sealion

      Public
      Sequenece alignment viewer
      JavaScript
      •
      Other
      •0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • fieldbioinformatics

      Public
      The ARTIC fieldbioinformatics pipeline
      Python
      •
      MIT License
      •90•127•6•1•Updated Dec 16, 2025Dec 16, 2025

    • amplicon-nf

      Public
      Amplicon genome assembly for ARTIC style primer schemes using Nextflow.
      Nextflow
      •
      MIT License
      •3•7•3•1•Updated Dec 10, 2025Dec 10, 2025

    • scylla

      Public
      single sample processing
      Python
      •
      GNU General Public License v3.0
      •6•10•6•4•Updated Dec 5, 2025Dec 5, 2025

    • primalscheme3

      Public
      Primalscheme3. Generation of highly multiplex primerschemes
      HTML
      •
      GNU General Public License v3.0
      •8•20•3•0•Updated Dec 4, 2025Dec 4, 2025

    • aiv_hosts

      Public
      A mapping of avian influenza host designation to species names
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Nov 12, 2025Nov 12, 2025

    • primal-page

      Public
      HTML
      •1•5•0•0•Updated Nov 6, 2025Nov 6, 2025

    • table-top

      Public
      System for delivering documents and data in an interactive training exercise
      HTML
      •
      MIT License
      •0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • ebolavirus

      Public
      A repository of information and resources about viruses in the genus Ebolavirus
      1•1•1•1•Updated Oct 16, 2025Oct 16, 2025

    • align_trim

      Public
      Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files.
      Python
      •
      MIT License
      •0•0•5•0•Updated Oct 16, 2025Oct 16, 2025

    • bed2idt

      Public
      Convert bedfiles to IDT custom spreadsheets
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Aug 22, 2025Aug 22, 2025

    • prepare-nf

      Public
      Generate a run sample sheet to input to amplicon-nf
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • squirrel-nf

      Public
      Interactive workflow to run squirrel
      Nextflow
      •
      GNU General Public License v3.0
      •1•0•1•0•Updated Aug 21, 2025Aug 21, 2025

    • website

      Public
      HTML
      •
      Other
      •6•3•0•1•Updated Jul 24, 2025Jul 24, 2025

    • primerscheme-specs

      Public
      Specifications for the primer.bed and reference.fasta file.
      Typst
      •
      MIT License
      •0•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • artic-mpxv-nf

      Public
      ARTIC Epi2me compatible workflow and reporting
      Nextflow
      •
      Other
      •36•3•1•1•Updated Jun 23, 2025Jun 23, 2025

    • civet

      Public
      Cluster Investigation & Virus Epidemiology Tool
      Python
      •
      GNU General Public License v3.0
      •14•50•32•0•Updated Jun 17, 2025Jun 17, 2025

    • artic-mpxv-illumina-nf

      Public
      Python
      •
      MIT License
      •4•5•0•0•Updated Apr 16, 2025Apr 16, 2025

    • rampart

      Public
      Read Assignment, Mapping, and Phylogenetic Analysis in Real Time
      JavaScript
      •
      GNU General Public License v3.0
      •34•82•28•17•Updated Mar 11, 2025Mar 11, 2025

    • rampart-nf

      Public
      Nextflow wrapper for RAMPART
      Nextflow
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 11, 2025Mar 11, 2025

    • phylofunk

      Public
      Java
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Mar 8, 2025Mar 8, 2025

    • aubergine

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

    • rampart-mpxv

      Public
      Dockerfile
      •1•0•0•0•Updated Mar 5, 2025Mar 5, 2025

    • primalpooling

      Public
      Collection of Scripts for the OT2 for pooling primers
      Python
      •0•1•0•0•Updated Dec 20, 2024Dec 20, 2024

    • artic-rsv

      Public
      Nextflow
      •5•5•5•0•Updated Aug 2, 2024Aug 2, 2024

    • artic-measles

      Public
      Repository for realtime sequencing of measles virus using the MinION
      5•1•2•0•Updated Sep 14, 2023Sep 14, 2023

    • rampart-nipah

      Public
      0•1•0•0•Updated Sep 14, 2023Sep 14, 2023

    • rampart-iva

      Public
      0•1•0•0•Updated Sep 14, 2023Sep 14, 2023

    • rampart-ebov

      Public
      A RAMPART protocol and environment for sequencing Ebola viruses
      1•1•0•0•Updated Sep 14, 2023Sep 14, 2023