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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

  • Genome-graph approach to identify large transposable elements called Starships: O'Donnell et al. 2024 bioRxiv
    • Refer to this repository for how to perform a similar genome-graph based analysis
    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 Public

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

    Shell 66 15

  2. PAQman Public

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

    Shell 2

  3. fusemblr Public

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

    Shell 2

  4. PhasedDiploidGenomeAssemblyPipeline Public

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

    R 21 1

  5. aneuploidy_detection Public

    Script uses simply alignment and a hard threshold for deviation in order to detect changes in coverage

    Shell 5 1

  6. pggb_starship_pipeline Public

    A pipeline for Starship (or any large PAV) discovery using genome-graphs

    1