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Achievements

Achievement: Pull SharkAchievement: StarstruckAchievement: Arctic Code Vault Contributor

Achievements

Achievement: Pull SharkAchievement: StarstruckAchievement: Arctic Code Vault Contributor

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SAMtoBAM/README.md

I am a genomicist interested in the evolution of genome structure and content
I primarily create tools or write repositories with lengthy explanations

Linux bash R Markdown Stars

Recent projects and pipelines

  • A comprehensive Starship and Starship-like region detection tool: stargraph

  • Linking a higher frequency of Starship presence with domesticated and pathogenic fungi: O'Donnell et al. 2024 bioRxiv
    • Refer to this repository for how to use genome-graphs to detect Starships
    Refer to this repository for easily generating accurate phylogenies from public genome datasets
    Refer to this repository for hypergeometric functional enrichment tests using COG annotations

  • ScRAP dataset with phased assemblies, a population SV dataset and complex aneuploidy: O'Donnell et al. 2023 Nat. Gen.
    • Refer to this repository for the detection of both simple and complex aneuploidy
    Refer to this repository for the phasing and assembling diploid heterozygotes

  • A whole genome alignment SV calling tool: MUM&Co O'Donnell and Fischer 2020 Bioinformatics
  • An ensemble reference-free assembly evaluation tool: PAQman

  • A complete automated assembly pipeline: fusemblr

  • A free-time project to track, visualise and compare peoples visitation of UNESCO sites
    • Refer to this repository for the shiny R app and input file

Pinned Loading

  1. MUMandCo MUMandCo Public

    MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation

    Shell 70 15

  2. stargraph stargraph Public

    A complete Starship and Starship-like region detection tool combining genome-graph based and starfish detection

    Shell 1

  3. PAQman PAQman Public

    PAQman is a tool for a reference-free and comprehensive evaluation of genome assemblies

    Shell 2

  4. fusemblr fusemblr Public

    fusemblr is a pipeline wrapper designed for the assembly of complex genomes using nanopore reads and paired-end illumina

    Shell 2

  5. PhasedDiploidGenomeAssemblyPipeline PhasedDiploidGenomeAssemblyPipeline Public

    Using de-novo assembly and read-phasing to assemble reference-free diploid genomes

    R 22 2

  6. aneuploidy_detection aneuploidy_detection Public

    Aneuploidy detection method for detecting both 'simple' and 'complex' aneuploidies

    Shell 5 1