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    52 repositories

    • peartree

      Public
      JavaScript
      •
      MIT License
      •2•27•4•0•Updated Apr 21, 2026Apr 21, 2026

    • fieldbioinformatics

      Public
      The ARTIC fieldbioinformatics pipeline
      Python
      •
      MIT License
      •91•131•3•1•Updated Apr 21, 2026Apr 21, 2026

    • amplicon-nf

      Public
      Amplicon genome assembly for ARTIC style primer schemes using Nextflow.
      Nextflow
      •
      MIT License
      •5•12•2•2•Updated Apr 10, 2026Apr 10, 2026

    • align_trim

      Public
      Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files.
      Python
      •
      MIT License
      •0•2•3•0•Updated Apr 9, 2026Apr 9, 2026

    • squirrel-nf

      Public
      Interactive workflow to run squirrel
      Nextflow
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Apr 8, 2026Apr 8, 2026

    • rampart-app

      Public
      JavaScript
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • raccoon

      Public
      Python
      •
      MIT License
      •0•1•1•0•Updated Mar 30, 2026Mar 30, 2026

    • raccoon-nf

      Public
      A nextflow implementation of https://github.com/aineniamh/raccoon
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • artic-doc

      Public
      HTML
      •
      Other
      •5•0•1•0•Updated Mar 30, 2026Mar 30, 2026

    • glacier-catalogue

      Public
      A catalogue of workflow repos available for Glacier application
      0•0•0•0•Updated Mar 23, 2026Mar 23, 2026

    • scylla

      Public
      single sample processing
      Python
      •
      GNU General Public License v3.0
      •7•10•6•3•Updated Mar 19, 2026Mar 19, 2026

    • sealion

      Public
      Sequenece alignment viewer
      JavaScript
      •
      Other
      •0•1•0•0•Updated Mar 12, 2026Mar 12, 2026

    • rampart

      Public
      Read Assignment, Mapping, and Phylogenetic Analysis in Real Time
      JavaScript
      •
      GNU General Public License v3.0
      •34•82•28•17•Updated Mar 2, 2026Mar 2, 2026

    • table-top

      Public
      System for delivering documents and data in an interactive training exercise
      HTML
      •
      MIT License
      •0•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • viz

      Public
      HTML
      •0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • beast-nf

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • primalscheme3

      Public
      Primalscheme3. Generation of highly multiplex primerschemes
      HTML
      •
      GNU General Public License v3.0
      •8•22•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•6•0•0•Updated Nov 6, 2025Nov 6, 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

    • bed2idt

      Public
      Convert bedfiles to IDT custom spreadsheets
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•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

    • 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•4•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-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
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