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    103 repositories

    • rvi-viral-metagenomics-pipeline

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • assorted-sub-workflows

      Public
      Nextflow
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • generate_mags

      Public
      Nextflow
      •
      MIT License
      •0•2•0•0•Updated Sep 12, 2025Sep 12, 2025

    • visiogen

      Public
      K-mer based probe design.
      Rust
      •
      GNU Affero General Public License v3.0
      •0•3•0•0•Updated Sep 10, 2025Sep 10, 2025

    • nextflow-commons

      Public
      Store of generic templates and scripts for nextflow pipelines
      Nextflow
      •
      GNU Affero General Public License v3.0
      •0•1•0•3•Updated Sep 9, 2025Sep 9, 2025

    • gps-pipeline-sanger

      Public
      Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)
      Nextflow
      •
      GNU General Public License v3.0
      •10•0•0•0•Updated Sep 9, 2025Sep 9, 2025

    • trepogeno

      Public
      mirror repository from gitlab for the wrapper script streamlining lineage calling with mykrobe
      Python
      •0•1•0•0•Updated Aug 29, 2025Aug 29, 2025

    • juno-app

      Public
      Static site for the Juno project
      JavaScript
      •0•0•0•2•Updated Aug 21, 2025Aug 21, 2025

    • Multiple-mappings-to-bam

      Public
      A GSoC project - Nextflow pipeline updating the legacy Python2 Multiple mappings to bam to nextflow.
      Python
      •
      GNU Affero General Public License v3.0
      •2•2•1•1•Updated Aug 13, 2025Aug 13, 2025

    • assembly_unicycler_short_read

      Public
      Assembly Unicycler Short Reads
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

    • assembly_flye_long_read

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • abundance_estimation

      Public
      Mirrored respository of abundance_estimation
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • ONTAP

      Public
      Nextflow pipeline for accurate pathogen typing from ONT amplicon sequencing data
      Nextflow
      •
      GNU Affero General Public License v3.0
      •0•4•0•0•Updated Jul 24, 2025Jul 24, 2025

    • python-work-experience

      Public
      Work Experience Exercises
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • redcap-helmchart

      Public
      HTML
      •
      Apache License 2.0
      •3•0•0•0•Updated Jul 1, 2025Jul 1, 2025

    • TpRNAseq

      Public
      A bacterial RNAseq pipeline, designed for analysis of Treponema pallidum data
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • enadownloader

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 17, 2025Jun 17, 2025

    • BinBaDGer

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 20, 2025May 20, 2025

    • BaGPipe

      Public
      A bacterial GWAS pipeline written in Nextflow that uses Pyseer; Part III Project for Systems Biology at the University of Cambridge
      Nextflow
      •
      MIT License
      •1•18•1•0•Updated Mar 25, 2025Mar 25, 2025

    • Fastaq

      Public
      Python3 scripts to manipulate FASTA and FASTQ files
      bioinformaticsresearchgenomicspathogensequencingnext-generation-sequencingglobal-healthinfectious-diseases
      Python
      •
      Other
      •21•71•8•2•Updated Mar 24, 2025Mar 24, 2025

    • pymummer

      Public
      Python3 module for running MUMmer and reading the output
      Python
      •
      Other
      •10•33•4•0•Updated Mar 24, 2025Mar 24, 2025

    • nextflowtool

      Public
      Groovy
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • Unicycler

      Public
      hybrid assembly pipeline for bacterial genomes
      C++
      •
      GNU General Public License v3.0
      •137•1•0•0•Updated Dec 19, 2024Dec 19, 2024

    • bactgen-training-app

      Public
      Static site for training on the Juno/GPS2 projects
      HTML
      •1•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • bentley-app

      Public
      Static site for Stephen Bentley's group
      JavaScript
      •0•0•0•1•Updated Nov 6, 2024Nov 6, 2024

    • nano-rave

      Public
      Nextflow pipeline designed for rapid onsite QC and variant calling of Oxford Nanopore data (following basecalling and demultiplexing with Guppy).
      Nextflow
      •
      GNU Affero General Public License v3.0
      •5•13•1•0•Updated Aug 9, 2024Aug 9, 2024

    • sh16_scripts

      Public archive
      Deprecated scripts for reference only
      Python
      •0•0•0•0•Updated Jul 18, 2024Jul 18, 2024

    • software-tracker

      Public
      API and helper scripts for the pathogen software installation tracking database
      Python
      •
      MIT License
      •1•0•1•0•Updated Jul 12, 2024Jul 12, 2024

    • Artemis

      Public
      Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
      bioinformaticsresearchgenomicspathogensequencingnext-generation-sequencingbioinformatics-pipelineglobal-healthinfectious-diseases
      Java
      •
      Other
      •77•255•29•4•Updated Jun 15, 2024Jun 15, 2024

    • Phylign

      Public
      Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on a laptop within a few hours.
      Python
      •
      Other
      •9•0•0•0•Updated May 22, 2024May 22, 2024