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    47 repositories

    • make_prg

      Public
      Code to create a PRG from a Multiple Sequence Alignment file
      Python
      •
      Other
      •7•25•11•3•Updated Sep 10, 2025Sep 10, 2025

    • pling

      Public
      Plasmid analysis using rearrangement distances
      JavaScript
      •
      MIT License
      •2•49•6•1•Updated Sep 4, 2025Sep 4, 2025

    • varifier

      Public
      Variant call verification
      Python
      •
      MIT License
      •3•16•7•0•Updated May 12, 2025May 12, 2025

    • viridian_simulations_workflow

      Public
      Workflow to simulate SARS-CoV-2 amplicons and reads.
      Python
      •
      MIT License
      •0•0•0•0•Updated May 8, 2025May 8, 2025

    • gramtools

      Public
      Genome inference from a population reference graph
      pythonc-plus-plusbioinformaticsvariant-callinggenome-graphembl-ebiprgreference-graph
      C++
      •
      MIT License
      •15•96•14•0•Updated Apr 1, 2025Apr 1, 2025

    • viridian

      Public
      Python
      •
      MIT License
      •6•23•26•0•Updated Mar 6, 2025Mar 6, 2025

    • cylon

      Public
      Virus assembler from amplicon sequencing reads
      Python
      •
      MIT License
      •1•5•1•0•Updated Mar 6, 2025Mar 6, 2025

    • pandora

      Public
      Pan-genome inference and genotyping with long noisy or short accurate reads
      C++
      •
      MIT License
      •15•119•74•0•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
      •16•20•6•1•Updated Nov 24, 2024Nov 24, 2024

    • clockwork

      Public
      CRyPTIC data processing pipelines
      HTML
      •
      MIT License
      •22•34•22•5•Updated Jul 18, 2024Jul 18, 2024

    • ivcfmerge

      Public
      A utility to merge a large number of VCF files incrementally
      vcfvcfsvcf-filesvariant-call-format
      Python
      •0•3•1•1•Updated Jul 9, 2024Jul 9, 2024

    • minos

      Public
      Variant call adjudication
      Python
      •
      MIT License
      •5•16•6•0•Updated Jun 13, 2024Jun 13, 2024

    • sprog

      Public
      Species Probes Generator
      Python
      •
      MIT License
      •2•9•0•0•Updated Jun 11, 2024Jun 11, 2024

    • paper_pfalciparum_DBs

      Public
      Python
      •
      MIT License
      •1•1•0•0•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
      •13•10•7•1•Updated Jun 13, 2023Jun 13, 2023

    • tb-sputum-project

      Public
      Pipeline to analyse the TB sputum data
      nanoporepipelinetuberculosissputum
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Dec 16, 2022Dec 16, 2022

    • neo4j_benchmark

      Public
      Jupyter Notebook
      •0•0•0•5•Updated Aug 23, 2022Aug 23, 2022

    • covid-truth-eval

      Public
      Evaluate accuracy of covid assemblies where truth is available
      Python
      •
      MIT License
      •1•3•0•0•Updated Aug 17, 2022Aug 17, 2022

    • minos-paper-benchmarking

      Public
      Python
      •
      MIT License
      •2•1•0•0•Updated Aug 11, 2022Aug 11, 2022

    • cluster_vcf_records

      Public
      Python package to cluster VCF records. Used by gramtools and minos
      Python
      •
      MIT License
      •4•1•2•1•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-pipelinetuberculosisantimicrobial-resistance-genes
      Python
      •3•7•3•0•Updated Jul 20, 2022Jul 20, 2022

    • py-cortex-api

      Public
      Python API for cortex
      Python
      •
      MIT License
      •3•1•0•0•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
      •567•0•0•0•Updated May 17, 2022May 17, 2022

    • covid-truth-datasets

      Public
      SARS-CoV-2 datasets for testing pipelines
      MIT License
      •0•2•0•0•Updated Apr 12, 2022Apr 12, 2022

    • triphecta

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Dec 17, 2021Dec 17, 2021

    • QCovid

      Public
      QC pipelines for sars-cov-2 sequence+consensus submitted to the ENA
      Jupyter Notebook
      •
      MIT License
      •0•2•2•0•Updated Dec 16, 2021Dec 16, 2021

    • paper_gramtools_nesting

      Public
      Python
      •1•1•0•0•Updated Aug 10, 2021Aug 10, 2021

    • paper_pandora2020_analyses

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•1•0•Updated Aug 2, 2021Aug 2, 2021

    • bigsi-ebi-api

      Public
      API service for EBI's BIGSI
      Python
      •1•2•0•0•Updated Jul 29, 2021Jul 29, 2021

    • pandora_paper_roc

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jun 21, 2021Jun 21, 2021