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    25 repositories

    • ncov2019-artic-nf

      Public
      A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
      Nextflow
      •
      GNU Affero General Public License v3.0
      •87•91•24•12•Updated Nov 8, 2023Nov 8, 2023

    • vapor

      Public
      Python
      •
      GNU General Public License v3.0
      •11•11•5•1•Updated Jun 29, 2023Jun 29, 2023

    • pengu-ddt

      Public
      A tool for interacting with the DIGEST project PostgreSQL database
      Python
      •0•1•0•3•Updated Dec 8, 2022Dec 8, 2022

    • aln2type

      Public
      Python
      •3•8•4•1•Updated Oct 13, 2022Oct 13, 2022

    • msa2vcf

      Public
      Python
      •3•2•1•2•Updated May 20, 2022May 20, 2022

    • grapevine_nextflow

      Public
      Nextflow implementation of grapevine
      Nextflow
      •3•0•0•0•Updated Mar 9, 2021Mar 9, 2021

    • snapper3

      Public
      partial reimplementation of snapperdb
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 19, 2021Jan 19, 2021

    • ncov-tools

      Public
      Small collection of tools for performing quality control on coronavirus sequencing data and genomes
      Python
      •
      MIT License
      •15•3•0•0•Updated Sep 9, 2020Sep 9, 2020

    • fieldbioinformatics

      Public
      The ARTIC field bioinformatics pipeline
      Python
      •
      MIT License
      •91•0•0•0•Updated Mar 9, 2020Mar 9, 2020

    • nextflow_pipelines

      Public
      Nextflow pipeline script, config and ancillary files for PHW PenGU sequencing
      Nextflow
      •2•3•0•0•Updated Dec 7, 2019Dec 7, 2019

    • prepareref_nextflow

      Public
      Mask recombination from reference sequences for SNP calling
      Nextflow
      •0•1•0•0•Updated Nov 21, 2019Nov 21, 2019

    • qc_nextflow

      Public
      A nextflow pipeline for inital QC of Illumina sequencing data
      Nextflow
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Oct 31, 2019Oct 31, 2019

    • singularity-recipes

      Public
      A collection of Singularity recipes useful for our nextflow pipelines
      Perl
      •1•5•0•0•Updated Oct 4, 2019Oct 4, 2019

    • PenGU-testdata-build

      Public
      Simulate fastq files from a list of RefSeq URLs
      Nextflow
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 8, 2019Jul 8, 2019

    • hash-cgmlst

      Public
      Python
      •
      Other
      •4•0•0•0•Updated Jun 26, 2019Jun 26, 2019

    • enterovirus-NF

      Public
      Nextflow pipeline for de novo assembly of enterovirus genomes
      Shell
      •0•1•0•0•Updated Jun 14, 2019Jun 14, 2019

    • vapor_benchmark_realdata

      Public
      Shell
      •0•1•0•0•Updated Mar 13, 2019Mar 13, 2019

    • vapor_benchmark_simulation

      Public
      HTML
      •0•1•0•0•Updated Mar 10, 2019Mar 10, 2019

    • vapor_benchmark_reassortment

      Public
      Shell
      •0•1•0•0•Updated Mar 10, 2019Mar 10, 2019

    • vapor_benchmark_mapping

      Public
      Shell
      •0•1•0•0•Updated Mar 10, 2019Mar 10, 2019

    • report-writer

      Public
      Python
      •0•1•0•0•Updated Feb 10, 2019Feb 10, 2019

    • connor-lab.github.io

      Public
      0•0•0•0•Updated Jan 17, 2019Jan 17, 2019

    • centrifuge-summary

      Public
      Summarise a Centrifuge (https://ccb.jhu.edu/software/centrifuge/manual.shtml) report for a specific taxon and its sub-taxa
      Python
      •0•1•0•0•Updated Dec 12, 2018Dec 12, 2018

    • connor-lab

      Public
      0•0•0•0•Updated Nov 2, 2018Nov 2, 2018

    • clockwork

      Public
      CRyPTIC data processing pipelines
      HTML
      •
      MIT License
      •22•0•0•0•Updated Aug 1, 2018Aug 1, 2018
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