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@CobiontID

CobiontID

Tools for detecting cobionts and contaminants in Darwin Tree of Life genomes

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  1. read_VAE read_VAE Public

    VAE-based framework to explore long-read datasets and identify potential contaminants or cobionts

    Python

  2. MarkerScan MarkerScan Public

    This repository contains a Snakemake pipeline which determines the species composition of the sample by SSU presence and separates them accordingly.

    Python 5 2

  3. kmer-counter kmer-counter Public

    A fast k-mer counter written in Rust

    Rust

Repositories

Showing 9 of 9 repositories
  • Kudoa_genomes Public

    Data associated with "Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution"

    CobiontID/Kudoa_genomes’s past year of commit activity
    0 0 0 0 Updated Nov 5, 2024
  • HiC_network Public

    Group and visualise networks of interacting sequences using chromatin contacts and graph embeddings

    CobiontID/HiC_network’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Nov 4, 2024
  • CobiontID.github.io Public
    CobiontID/CobiontID.github.io’s past year of commit activity
    Jupyter Notebook 2 0 0 0 Updated Nov 4, 2024
  • read_VAE Public

    VAE-based framework to explore long-read datasets and identify potential contaminants or cobionts

    CobiontID/read_VAE’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 25, 2024
  • MarkerScan Public

    This repository contains a Snakemake pipeline which determines the species composition of the sample by SSU presence and separates them accordingly.

    CobiontID/MarkerScan’s past year of commit activity
    Python 5 2 1 1 Updated Jul 11, 2024
  • WolbachiaSubmission Public
    CobiontID/WolbachiaSubmission’s past year of commit activity
    Python 0 1 0 1 Updated Jul 11, 2024
  • unique-kmer-counts Public

    Count the number of distinct k-mers in a sequence

    CobiontID/unique-kmer-counts’s past year of commit activity
    Rust 0 MIT 0 0 0 Updated Jun 3, 2024
  • kmer-counter Public

    A fast k-mer counter written in Rust

    CobiontID/kmer-counter’s past year of commit activity
    Rust 0 MIT 0 0 0 Updated Jun 3, 2024
  • fastk-medians Public Forked from thegenemyers/FASTK

    Calculate median number of times each k-mer in a sequence occurs across a set

    CobiontID/fastk-medians’s past year of commit activity
    C 0 16 0 0 Updated Feb 7, 2023

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