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    34 repositories

    • bed2idt

      Public
      Convert bedfiles to IDT custom spreadsheets
      Python
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • primalpooling

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

    • primal-page

      Public
      HTML
      •0•2•0•0•Updated Dec 20, 2024Dec 20, 2024

    • fieldbioinformatics

      Public
      The ARTIC field bioinformatics pipeline
      Python
      •
      MIT License
      •88•117•1•4•Updated Dec 18, 2024Dec 18, 2024

    • website

      Public
      HTML
      •
      Other
      •6•2•0•1•Updated Dec 12, 2024Dec 12, 2024

    • artic-mpxv-nf

      Public
      ARTIC Epi2me compatible workflow and reporting
      Nextflow
      •
      Other
      •35•3•0•1•Updated Dec 10, 2024Dec 10, 2024

    • scylla

      Public
      single sample processing
      Python
      •
      GNU General Public License v3.0
      •4•4•7•0•Updated Dec 9, 2024Dec 9, 2024

    • primalscheme3

      Public
      Primalscheme3. Generation of highly multiplex primerschemes
      Python
      •
      GNU General Public License v3.0
      •1•5•1•0•Updated Dec 7, 2024Dec 7, 2024

    • artic-mpxv-illumina-nf

      Public
      Python
      •
      MIT License
      •4•2•0•0•Updated Nov 21, 2024Nov 21, 2024

    • squirrel-nf

      Public
      Interactive workflow to run squirrel
      Nextflow
      •
      GNU General Public License v3.0
      •1•0•1•0•Updated Nov 11, 2024Nov 11, 2024

    • rampart

      Public
      Read Assignment, Mapping, and Phylogenetic Analysis in Real Time
      JavaScript
      •
      GNU General Public License v3.0
      •33•79•28•17•Updated Aug 21, 2024Aug 21, 2024

    • rampart-mpxv

      Public
      Dockerfile
      •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

    • artic-rsv

      Public
      Nextflow
      •1•4•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

    • primer-schemes

      Public
      Primer schemes for real-time genome epidemiology
      Python
      •
      Creative Commons Attribution 4.0 International
      •42•27•1•0•Updated Jun 14, 2023Jun 14, 2023

    • artic-ncov2019

      Public
      ARTIC nanopore protocol for nCoV2019 novel coronavirus
      Python
      •
      Creative Commons Attribution 4.0 International
      •165•167•44•2•Updated Mar 22, 2023Mar 22, 2023

    • civet

      Public
      Cluster Investigation & Virus Epidemiology Tool
      Python
      •
      GNU General Public License v3.0
      •14•49•32•0•Updated Dec 3, 2022Dec 3, 2022

    • artic-live

      Public
      HTML
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Oct 25, 2022Oct 25, 2022

    • polecat

      Public
      Python
      •
      GNU General Public License v3.0
      •1•9•1•0•Updated Feb 27, 2021Feb 27, 2021

    • Porechop

      Public
      adapter trimmer for Oxford Nanopore reads
      C++
      •
      GNU General Public License v3.0
      •130•7•0•1•Updated Nov 15, 2020Nov 15, 2020

    • lab-on-an-SSD

      Public
      Scripts for building the ARTIC lab-on-an-SSD
      Shell
      •
      MIT License
      •3•11•1•0•Updated Sep 9, 2020Sep 9, 2020

    • artic-ebov

      Public
      Repository of documents and data for Ebola virus
      Python
      •9•5•9•0•Updated Sep 4, 2020Sep 4, 2020

    • readucks

      Public
      Nanopore read de-multiplexer
      Python
      •
      GNU General Public License v3.0
      •3•13•0•0•Updated Mar 25, 2020Mar 25, 2020

    • artic-base

      Public template
      A base template for an implementation of an ARTIC install. This can be forked and modified for specific use-cases.
      1•7•0•0•Updated Jan 9, 2020Jan 9, 2020

    • artic-nipah

      Public
      ARTIC real-time package for Nipah virus (NiV)
      0•0•0•0•Updated Jan 8, 2020Jan 8, 2020

    • rampart-denv2

      Public
      0•1•0•0•Updated Dec 3, 2019Dec 3, 2019

    • artic-workshop

      Public
      Repository of material for the ARTIC workshop on real-time sequencing for outbreak response.
      Python
      •
      MIT License
      •3•1•0•0•Updated Dec 14, 2018Dec 14, 2018