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    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.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

    • 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 Dec 1, 2024Dec 1, 2024

    • repgenr

      Public
      RepGenR (Representative-Genome Repositories) clusters genome sequences based on average nucleotide identity to produce flexible databases
      Python
      •1•1•0•0•Updated Nov 27, 2024Nov 27, 2024

    • 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

    • 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.
      nanoporesequencingmetagenomicsbioinformatics
      Python
      •
      GNU General Public License v3.0
      •2•15•1•0•Updated Oct 4, 2024Oct 4, 2024

    • CanSNPer2

      Public
      CanSNPer2: A toolkit for SNP-typing bacterial genomes.
      Python
      •
      GNU General Public License v3.0
      •2•6•21•0•Updated Jan 17, 2024Jan 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 )
      taxonomic-classificationsamplicon16scustom-taxonomycustom-databasemetagenomic-classificationcentrifugetaxonomic-classificationgtdbganon
      Python
      •
      GNU General Public License v3.0
      •8•65•6•1•Updated Nov 21, 2023Nov 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.
      ncbisrasourmash
      Python
      •
      GNU General Public License v3.0
      •0•1•0•1•Updated Oct 11, 2023Oct 11, 2023

    • useful-scripts

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

    • NanoCLUST

      Public
      NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
      Nextflow
      •
      MIT License
      •49•0•0•0•Updated Feb 23, 2021Feb 23, 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, python 2 support is depricated) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Fou…
      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