Repositories list

• pling

  Public
  Plasmid analysis using rearrangement distances

  Python

  •

  MIT License

  •22 forks•5252 stars•33 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• make_prg

  Public
  Code to create a PRG from a Multiple Sequence Alignment file

  Python

  •

  Other

  •77 forks•2525 stars•1111 issues•33 pull requests•Updated Sep 10, 2025Sep 10, 2025

• varifier

  Public
  Variant call verification

  Python

  •

  MIT License

  •33 forks•1717 stars•77 issues•00 pull requests•Updated May 12, 2025May 12, 2025

• viridian_simulations_workflow

  Public
  Workflow to simulate SARS-CoV-2 amplicons and reads.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 8, 2025May 8, 2025

• gramtools

  Public
  Genome inference from a population reference graph

  pythonc-plus-plusbioinformatics+ 5

  pythonc-plus-plusbioinformaticsvariant-callinggenome-graphembl-ebiprgreference-graph

  C++

  •

  MIT License

  •1515 forks•9696 stars•1414 issues•00 pull requests•Updated Apr 1, 2025Apr 1, 2025

• viridian

  Public
  Python

  •

  MIT License

  •66 forks•3030 stars•2626 issues•00 pull requests•Updated Mar 6, 2025Mar 6, 2025

• cylon

  Public
  Virus assembler from amplicon sequencing reads

  Python

  •

  MIT License

  •11 fork•55 stars•11 issue•00 pull requests•Updated Mar 6, 2025Mar 6, 2025

• pandora

  Public
  Pan-genome inference and genotyping with long noisy or short accurate reads

  C++

  •

  MIT License

  •1515 forks•120120 stars•7474 issues•00 pull requests•Updated Dec 13, 2024Dec 13, 2024

• cobs

  Public
  COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

  C++

  •

  MIT License

  •1616 forks•2020 stars•66 issues•11 pull request•Updated Nov 24, 2024Nov 24, 2024

• clockwork

  Public
  CRyPTIC data processing pipelines

  HTML

  •

  MIT License

  •2222 forks•3434 stars•2222 issues•55 pull requests•Updated Jul 18, 2024Jul 18, 2024

• ivcfmerge

  Public
  A utility to merge a large number of VCF files incrementally

  vcfvcfsvcf-files+ 1

  vcfvcfsvcf-filesvariant-call-format

  Python

  •00 forks•33 stars•11 issue•11 pull request•Updated Jul 9, 2024Jul 9, 2024

• minos

  Public
  Variant call adjudication

  Python

  •

  MIT License

  •55 forks•1717 stars•66 issues•00 pull requests•Updated Jun 13, 2024Jun 13, 2024

• sprog

  Public
  Species Probes Generator

  Python

  •

  MIT License

  •22 forks•99 stars•00 issues•00 pull requests•Updated Jun 11, 2024Jun 11, 2024

• paper_pfalciparum_DBs

  Public
  Python

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Mar 8, 2024Mar 8, 2024

• BIGSI

  Public
  BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data

  Python

  •

  MIT License

  •1313 forks•1010 stars•77 issues•11 pull request•Updated Jun 13, 2023Jun 13, 2023

• tb-sputum-project

  Public
  Pipeline to analyse the TB sputum data

  nanoporepipelinetuberculosis+ 1

  nanoporepipelinetuberculosissputum

  Jupyter Notebook

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Dec 16, 2022Dec 16, 2022

• neo4j_benchmark

  Public archive
  Jupyter Notebook

  •00 forks•00 stars•00 issues•55 pull requests•Updated Aug 23, 2022Aug 23, 2022

• covid-truth-eval

  Public
  Evaluate accuracy of covid assemblies where truth is available

  Python

  •

  MIT License

  •11 fork•33 stars•00 issues•00 pull requests•Updated Aug 17, 2022Aug 17, 2022

• minos-paper-benchmarking

  Public
  Python

  •

  MIT License

  •22 forks•11 star•00 issues•00 pull requests•Updated Aug 11, 2022Aug 11, 2022

• cluster_vcf_records

  Public
  Python package to cluster VCF records. Used by gramtools and minos

  Python

  •

  MIT License

  •44 forks•11 star•22 issues•11 pull request•Updated Aug 9, 2022Aug 9, 2022

• Mykrobe_tb_workflow

  Public
  A workflow for analysis and resistance profiling of Mycobacterium tuberculosis nanopore data with Mykrobe

  bioinformaticsnanoporebioinformatics-pipeline+ 2

  bioinformaticsnanoporebioinformatics-pipelinetuberculosisantimicrobial-resistance-genes

  Python

  •33 forks•77 stars•33 issues•00 pull requests•Updated Jul 20, 2022Jul 20, 2022

• py-cortex-api

  Public
  Python API for cortex

  Python

  •

  MIT License

  •33 forks•11 star•00 issues•00 pull requests•Updated May 18, 2022May 18, 2022

• bwa

  Public
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

  C

  •

  GNU General Public License v3.0

  •579579 forks•00 stars•00 issues•00 pull requests•Updated May 17, 2022May 17, 2022

• covid-truth-datasets

  Public
  SARS-CoV-2 datasets for testing pipelines

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 12, 2022Apr 12, 2022

• triphecta

  Public
  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Dec 17, 2021Dec 17, 2021

• QCovid

  Public
  QC pipelines for sars-cov-2 sequence+consensus submitted to the ENA

  Jupyter Notebook

  •

  MIT License

  •00 forks•22 stars•22 issues•00 pull requests•Updated Dec 16, 2021Dec 16, 2021

• paper_gramtools_nesting

  Public
  Python

  •11 fork•11 star•00 issues•00 pull requests•Updated Aug 10, 2021Aug 10, 2021

• paper_pandora2020_analyses

  Public
  Jupyter Notebook

  •

  MIT License

  •11 fork•00 stars•11 issue•00 pull requests•Updated Aug 2, 2021Aug 2, 2021

• bigsi-ebi-api

  Public
  API service for EBI's BIGSI

  Python

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jul 29, 2021Jul 29, 2021

• pandora_paper_roc

  Public
  Jupyter Notebook

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 21, 2021Jun 21, 2021