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    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,…
      bioinformaticsnanoporesequencing
      bioinformaticsnanoporesequencingmetagenomics
      Python
      •
      GNU General Public License v3.0
      •3•20•1•0•Updated Jun 23, 2026Jun 23, 2026

    • neoswga

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jun 23, 2026Jun 23, 2026

    • nanometanf

      Public
      Backend of Nanometa-Live
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Jun 19, 2026Jun 19, 2026

    • metadarkmatter

      Public
      Detect novel bacterial taxa in metagenomic data using ANI-weighted placement uncertainty. Distinguishes true novelty from taxonomic ambiguity by combining compe…
      metagenomicsednaenvironmental-dna
      metagenomicsednaenvironmental-dnanovel-speciesmicrobial-dark-matterbiosurveillance
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 17, 2026Jun 17, 2026

    • flextaxd

      Public
      FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, g…
      ncbi-taxonomytaxonomic-classificationsamplicon
      ncbi-taxonomytaxonomic-classificationsamplicon16sncbi-databasecustom-taxonomycustom-databasemetagenomic-classificationcentrifugetaxonomic-classification
      Python
      •
      GNU General Public License v3.0
      •8•68•3•0•Updated Jun 4, 2026Jun 4, 2026

    • nanorunner

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 30, 2026May 30, 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…
      ncbisrasourmash
      ncbisrasourmash
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Apr 4, 2026Apr 4, 2026

    • NJRS

      Public
      NJRS (Neighbour-Joining Read-support) constructs phylogenetic trees for user-defined dataset groups using BAM-files. Supports low-frequency and homoplasy-associ…
      Python
      •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

    • taxbencher

      Public
      taxbencher: A Nextflow framework for benchmarking metagenomic taxonomic classifiers and profilers.
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Nov 29, 2025Nov 29, 2025

    • NanoPulse

      Public
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Nov 18, 2025Nov 18, 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…
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • merpcr

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 13, 2025Oct 13, 2025

    • baitUtils

      Public
      baitUtils is a comprehensive toolkit for the analysis and visualization of bait sequences used in in-solution hybridization
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 28, 2025Aug 28, 2025

    • repgenr

      Public
      RepGenR (Representative-Genome Repositories) clusters genome sequences based on average nucleotide identity to produce flexible databases
      Python
      •2•3•0•0•Updated Apr 4, 2025Apr 4, 2025

    • flexmetr

      Public
      FlexMetR (Flexible Metadata Resources) lets you add metadata to accession numbers or custom identifiers.
      Python
      •0•0•0•0•Updated Mar 31, 2025Mar 31, 2025

    • CanSNPer2-data

      Public
      Repository for the CanSNP database contaning the source tree from CanSNPer version 2 and later
      0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • CanSNPer2

      Public
      CanSNPer2: A toolkit for SNP-typing bacterial genomes.
      Python
      •
      GNU General Public License v3.0
      •3•5•23•0•Updated Jan 17, 2024Jan 17, 2024

    • useful-scripts

      Public
      A collection of useful scripts
      Perl
      •0•0•0•0•Updated Dec 8, 2021Dec 8, 2021

    • 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, pyt…
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 9, 2019Dec 9, 2019

    • STARPS

      Public
      A simulation tool for cultivation of bacterial populations
      C
      •0•1•0•0•Updated Nov 21, 2019Nov 21, 2019

    • MicrobialForensics

      Public
      A likelihood ratio-based approach for improved source attribution in microbial forensics
      Perl
      •0•0•0•0•Updated Oct 22, 2018Oct 22, 2018

    • MST

      Public
      Python
      •0•0•0•0•Updated Jan 25, 2018Jan 25, 2018

    • Predators-and-nutrient-availability-favor-protozoa-resisting-bacteria-in-aquatic-systems

      Public
      R
      •0•0•0•0•Updated Jan 24, 2018Jan 24, 2018
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