Repositories list

• scylla

  Public
  single sample processing

  Python

  •

  GNU General Public License v3.0

  •4•4•4•0•Updated Nov 15, 2024Nov 15, 2024

• artic-mpxv-nf

  Public
  ARTIC Epi2me compatible workflow and reporting

  Nextflow

  •

  Other

  •35•1•0•0•Updated Nov 14, 2024Nov 14, 2024

• fieldbioinformatics

  Public
  The ARTIC field bioinformatics pipeline

  Python

  •

  MIT License

  •88•116•0•5•Updated Nov 14, 2024Nov 14, 2024

• website

  Public
  HTML

  •

  Other

  •6•2•0•1•Updated Nov 12, 2024Nov 12, 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

• artic-mpxv-illumina-nf

  Public
  Python

  •

  MIT License

  •4•2•0•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•3•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

  •41•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•8•1•0•Updated Feb 27, 2021Feb 27, 2021

• Porechop

  Public
  adapter trimmer for Oxford Nanopore reads

  C++

  •

  GNU General Public License v3.0

  •128•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

• ebolavirus

  Public
  A repository of information and resources about viruses in the genus Ebolavirus

  1•1•1•0•Updated Oct 28, 2018Oct 28, 2018

• nanopolish

  Public
  Signal-level algorithms for MinION data

  C++

  •

  MIT License

  •159•0•0•0•Updated Jun 4, 2018Jun 4, 2018

• ebov_drc_2018

  Public
  0•0•0•0•Updated May 15, 2018May 15, 2018

• fieldlab

  Public
  Descriptions of the ARTIC field laboratory

  1•0•0•0•Updated Feb 26, 2018Feb 26, 2018