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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 65 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 15 2

  3. CanSNPer2 CanSNPer2 Public

    CanSNPer2: A toolkit for SNP-typing bacterial genomes.

    Python 6 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 15 repositories
  • 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 0 0 0 Updated Dec 10, 2024
  • 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 Dec 1, 2024
  • 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 Nov 27, 2024
  • CanSNPer2-data Public

    Repository for the CanSNP database contaning the source tree from CanSNPer version 2 and later

    FOI-Bioinformatics/CanSNPer2-data’s past year of commit activity
    0 0 0 0 Updated Oct 11, 2024
  • 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 15 GPL-3.0 2 1 0 Updated Oct 4, 2024
  • CanSNPer2 Public

    CanSNPer2: A toolkit for SNP-typing bacterial genomes.

    FOI-Bioinformatics/CanSNPer2’s past year of commit activity
    Python 6 GPL-3.0 2 21 0 Updated Jan 17, 2024
  • 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 65 GPL-3.0 8 6 1 Updated Nov 21, 2023
  • 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 1 Updated Oct 11, 2023
  • useful-scripts Public

    A collection of useful scripts

    FOI-Bioinformatics/useful-scripts’s past year of commit activity
    Perl 0 0 0 0 Updated Dec 8, 2021
  • NanoCLUST Public Forked from genomicsITER/NanoCLUST

    NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads

    FOI-Bioinformatics/NanoCLUST’s past year of commit activity
    Nextflow 0 MIT 49 0 0 Updated Feb 23, 2021
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