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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 of pipelines and code in order that others can be inspired to use part or all of the pipeline in their own analyses

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 whole genome alignment SV detection tool
    Refer to this repository for the detection of both simple and complex aneuploidy
    Refer to this repository for the phasing and assembling diploid heterozygotes
  • An ensemble reference-free assembly evaluationtool
  • A complete automated assembly pipeline
  • 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 66 15

  2. PAQman PAQman Public

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

    Shell 2

  3. fusemblr fusemblr Public

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

    Shell 1

  4. PhasedDiploidGenomeAssemblyPipeline PhasedDiploidGenomeAssemblyPipeline Public

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

    R 21 1

  5. aneuploidy_detection 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 pggb_starship_pipeline Public

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

    1