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FOI-Bioinformatics

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  1. flextaxd flextaxd Public

    FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

    Python 67 8

  2. nanometa_live nanometa_live Public

    A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineered for precision, speed, and user-friendliness, with offline …

    Python 20 3

  3. CanSNPer2 CanSNPer2 Public

    CanSNPer2: A toolkit for SNP-typing bacterial genomes.

    Python 5 2

  4. repgenr repgenr Public

    RepGenR (Representative-Genome Repositories) clusters genome sequences based on average nucleotide identity to produce flexible databases

    Python 3 1

  5. STARPS STARPS Public

    A simulation tool for cultivation of bacterial populations

    C 1

  6. cansnper1.1 cansnper1.1 Public

    CanSNPer1.1: A toolkit for SNP-typing using NGS data. Copyright (C) 2016 Adrian Lärkeryd Updates done by David Sundell VERSION 1.1.0 (Adjusted to python 3, python 2 support is depricated) This prog…

    Python 1

Repositories

Showing 10 of 23 repositories
  • nanometa_live Public

    A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineered for precision, speed, and user-friendliness, with offline functionality post-initialization.

    FOI-Bioinformatics/nanometa_live’s past year of commit activity
    Python 20 GPL-3.0 3 1 0 Updated May 7, 2026
  • nanometanf Public

    Backend of Nanometa-Live

    FOI-Bioinformatics/nanometanf’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated May 7, 2026
  • nanorunner Public
    FOI-Bioinformatics/nanorunner’s past year of commit activity
    Python 0 MIT 0 0 0 Updated May 7, 2026
  • neoswga Public
    FOI-Bioinformatics/neoswga’s past year of commit activity
    Python 0 AGPL-3.0 0 0 0 Updated Apr 21, 2026
  • metaquest Public

    MetaQuest is a robust and user-friendly command-line toolkit designed to simplify and streamline the analysis of metagenomic data. From summarizing the presence of specific genomes to visualizing complex datasets, MetaQuest offers an array of tools to help researchers uncover insights from their metagenomic datasets.

    FOI-Bioinformatics/metaquest’s past year of commit activity
    Python 1 GPL-3.0 0 0 0 Updated Apr 4, 2026
  • metadarkmatter Public

    Detect novel bacterial taxa in metagenomic data using ANI-weighted placement uncertainty. Distinguishes true novelty from taxonomic ambiguity by combining competitive read recruitment with genome-genome ANI matrices. Species/genus classification with literature-backed thresholds.

    FOI-Bioinformatics/metadarkmatter’s past year of commit activity
    Python 1 GPL-3.0 0 0 0 Updated Apr 4, 2026
  • flextaxd Public

    FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

    FOI-Bioinformatics/flextaxd’s past year of commit activity
    Python 67 GPL-3.0 8 3 0 Updated Mar 15, 2026
  • NJRS Public

    NJRS (Neighbour-Joining Read-support) constructs phylogenetic trees for user-defined dataset groups using BAM-files. Supports low-frequency and homoplasy-associated SNPs.

    FOI-Bioinformatics/NJRS’s past year of commit activity
    Python 0 0 0 0 Updated Jan 27, 2026
  • taxbencher Public

    taxbencher: A Nextflow framework for benchmarking metagenomic taxonomic classifiers and profilers.

    FOI-Bioinformatics/taxbencher’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Nov 29, 2025
  • NanoPulse Public
    FOI-Bioinformatics/NanoPulse’s past year of commit activity
    Nextflow 0 MIT 0 2 0 Updated Nov 18, 2025
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