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@FOI-Bioinformatics

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 9

  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 18 3

  3. CanSNPer2 CanSNPer2 Public

    CanSNPer2: A toolkit for SNP-typing bacterial genomes.

    Python 5 2

  4. STARPS STARPS Public

    A simulation tool for cultivation of bacterial populations

    C 1

  5. 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

  6. repgenr repgenr Public

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

    Python 1 1

Repositories

Showing 10 of 19 repositories
  • taxbencher Public

    taxbench: 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 Oct 10, 2025
  • nanometanf Public

    Backend of Nanometa-Live

    FOI-Bioinformatics/nanometanf’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Oct 8, 2025
  • nanorunner Public
    FOI-Bioinformatics/nanorunner’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 28, 2025
  • 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 Sep 16, 2025
  • merpcr Public
    FOI-Bioinformatics/merpcr’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Sep 15, 2025
  • preprimer Public

    Prepare primers from different formats, i.e. schemes for tiled sequencing from varvamp to artic format. Also prepares and aligns primers with mepcr or exonerate.

    FOI-Bioinformatics/preprimer’s past year of commit activity
    Python 0 GPL-3.0 1 0 1 Updated Sep 11, 2025
  • baitUtils Public

    baitUtils is a comprehensive toolkit for the analysis and visualization of bait sequences used in in-solution hybridization

    FOI-Bioinformatics/baitUtils’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Aug 28, 2025
  • repgenr Public

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

    FOI-Bioinformatics/repgenr’s past year of commit activity
    Python 1 1 0 0 Updated Apr 4, 2025
  • flexmetr Public

    FlexMetR (Flexible Metadata Resources) lets you add metadata to accession numbers or custom identifiers.

    FOI-Bioinformatics/flexmetr’s past year of commit activity
    Python 0 0 0 0 Updated Mar 31, 2025
  • 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 9 3 0 Updated Mar 12, 2025
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