Repositories list

• 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•21•1•3•Updated Jan 6, 2026Jan 6, 2026

• TpRNAseq

  Public
  A bacterial RNAseq pipeline, designed for analysis of Treponema pallidum data

  Nextflow

  •

  MIT License

  •1•2•0•1•Updated Jan 6, 2026Jan 6, 2026

• 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

  bioinformaticsresearchgenomics+ 6pathogensequencingnext-generation-sequencingbioinformatics-pipelineglobal-healthinfectious-diseases

  Java

  •

  Other

  •77•260•29•5•Updated Dec 19, 2025Dec 19, 2025

• juno-app

  Public
  Static site for the Juno project

  JavaScript

  •0•0•0•3•Updated Nov 18, 2025Nov 18, 2025

• BinBaDGer

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 6, 2025Nov 6, 2025

• generate_mags

  Public
  Nextflow

  •

  MIT License

  •0•2•0•0•Updated Nov 4, 2025Nov 4, 2025

• Roary

  Public
  Rapid large-scale prokaryote pan genome analysis

  bioinformaticsresearchgenomics+ 6pathogensequencingnext-generation-sequencingbioinformatics-pipelineglobal-healthinfectious-diseases

  Perl

  •

  Other

  •191•363•192•0•Updated Nov 3, 2025Nov 3, 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 Oct 17, 2025Oct 17, 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•0•Updated Oct 16, 2025Oct 16, 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 29, 2025Sep 29, 2025

• assorted-sub-workflows

  Public
  Nextflow

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

• rvi-viral-metagenomics-pipeline

  Public
  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Sep 12, 2025Sep 12, 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

• 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

  •6•0•0•0•Updated Jul 1, 2025Jul 1, 2025

• enadownloader

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 17, 2025Jun 17, 2025

• Fastaq

  Public
  Python3 scripts to manipulate FASTA and FASTQ files

  bioinformaticsresearchgenomics+ 5pathogensequencingnext-generation-sequencingglobal-healthinfectious-diseases

  Python

  •

  Other

  •21•72•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

  •139•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

• 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