ARTICnetwork

This is the ARTICnetwork project, a Wellcome Trust funded project to provide a system for real-time genomic epidemiology of virus outbreaks.

Pinned Repositories

artic-base
A base template for an implementation of an ARTIC install. This can be forked and modified for specific use-cases.
7 7 01
artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
Language:Python170 32 81164
civet
Cluster Investigation & Virus Epidemiology Tool
Language:Python50 7 12814
fieldbioinformatics
The ARTIC fieldbioinformatics pipeline
Language:Python125 13 9369
lab-on-an-SSD
Scripts for building the ARTIC lab-on-an-SSD
Language:Shell11 9 13
polecat
Language:Python9 8 11
primalscheme3
Primalscheme3. Generation of highly multiplex primerschemes
Language:HTML134
primer-schemes
Primer schemes for real-time genome epidemiology
Language:Python27 11 942
rampart
Read Assignment, Mapping, and Phylogenetic Analysis in Real Time
Language:JavaScript80 15 8533
readucks
Nanopore read de-multiplexer
Language:Python13 5 14

ARTICnetwork's Repositories

artic-network/artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
Language:Python170 32 81164
artic-network/fieldbioinformatics
The ARTIC fieldbioinformatics pipeline
Language:Python125 13 9369
artic-network/rampart
Read Assignment, Mapping, and Phylogenetic Analysis in Real Time
Language:JavaScript80 15 8533
artic-network/civet
Cluster Investigation & Virus Epidemiology Tool
Language:Python50 7 12814
artic-network/primer-schemes
Primer schemes for real-time genome epidemiology
Language:Python27 11 942
artic-network/primalscheme3
Primalscheme3. Generation of highly multiplex primerschemes
Language:HTML134
artic-network/readucks
Nanopore read de-multiplexer
Language:Python13 5 14
artic-network/lab-on-an-SSD
Scripts for building the ARTIC lab-on-an-SSD
Language:Shell11 9 13
artic-network/polecat
Language:Python9 8 11
artic-network/Porechop
adapter trimmer for Oxford Nanopore reads
Language:C++7 4 07
artic-network/artic-ebov
Repository of documents and data for Ebola virus
Language:Python5 6 139
artic-network/artic-rsv
Language:Nextflow5 3 52
artic-network/scylla
single sample processing
Language:Python4 1 434
artic-network/artic-mpxv-nf
ARTIC Epi2me compatible workflow and reporting
Language:Nextflow3 2 01
artic-network/artic-mpxv-illumina-nf
Language:Python2 1 02
artic-network/primal-page
Language:HTML2 1 20
artic-network/website
Language:HTML2 10 06
artic-network/artic-measles
Repository for realtime sequencing of measles virus using the MinION
1 7 25
artic-network/ebolavirus
A repository of information and resources about viruses in the genus Ebolavirus
1 7 11
artic-network/primalpooling
Collection of Scripts for the OT2 for pooling primers
Language:Python1 1 0
artic-network/rampart-ebov
A RAMPART protocol and environment for sequencing Ebola viruses
1 5 01
artic-network/rampart-iva
1 6 0
artic-network/rampart-nipah
1 6 0
artic-network/bed2idt
Convert bedfiles to IDT custom spreadsheets
Language:Python00
artic-network/artic-live
Language:HTML5 0
artic-network/aubergine
Language:Nextflow
artic-network/phylofunk
Language:Java
artic-network/rampart-mpxv
Language:Dockerfile2 01
artic-network/rampart-nf
Nextflow wrapper for RAMPART
Language:Nextflow
artic-network/squirrel-nf
Interactive workflow to run squirrel
Language:Nextflow3 11