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@logsdon-lab

Logsdon Lab

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  1. CenMAP CenMAP Public

    Centromere mapping and annotation pipeline

    Python 23 2

  2. NucFlag NucFlag Public

    Misassembly Identifier

    Python 16 1

  3. CenPlot CenPlot Public

    Centromere plotting library

    Python 4 1

  4. AssemblyRepairer AssemblyRepairer Public

    Forked from gaoshenghanpenn/AssemblyRepairer

    Python 4

  5. CenStats CenStats Public

    Centromere statistics toolkit

    Python 1

  6. Snakemake-ONT-Basecalling Snakemake-ONT-Basecalling Public

    Snakemake workflow to basecall ONT reads with dorado.

    Python 1

Repositories

Showing 10 of 29 repositories
  • ont-data-storage Public

    Documentation and scripts for storing ONT promethION sequencing data on UPenn's LPC and AWS

    logsdon-lab/ont-data-storage’s past year of commit activity
    Python 0 0 0 0 Updated Mar 10, 2026
  • Snakemake-CutNRun Public

    Workflow to visualize CUT&RUN data

    logsdon-lab/Snakemake-CutNRun’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Mar 10, 2026
  • Snakemake-Assembly Public

    Workflow to generate hifiasm and verkko assemblies.

    logsdon-lab/Snakemake-Assembly’s past year of commit activity
    Python 0 0 1 0 Updated Mar 9, 2026
  • NucFlag Public

    Misassembly Identifier

    logsdon-lab/NucFlag’s past year of commit activity
    Python 16 MIT 1 3 0 Updated Mar 4, 2026
  • rs-nucflag Public

    NucFlag library

    logsdon-lab/rs-nucflag’s past year of commit activity
    Rust 0 MIT 0 2 0 Updated Mar 3, 2026
  • CenMAP Public

    Centromere mapping and annotation pipeline

    logsdon-lab/CenMAP’s past year of commit activity
    Python 23 MIT 2 1 1 Updated Feb 28, 2026
  • Snakemake-NucFlag Public

    Workflow to map PacBio HiFi reads back to an assembly and check for misassemblies at specific regions via NucFlag.

    logsdon-lab/Snakemake-NucFlag’s past year of commit activity
    Python 0 1 0 0 Updated Feb 27, 2026
  • Snakemake-MutationRate Public

    Workflow to calculate mutation rate of a reference region relative to multiple query regions

    logsdon-lab/Snakemake-MutationRate’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 21, 2026
  • CenPlot Public

    Centromere plotting library

    logsdon-lab/CenPlot’s past year of commit activity
    Python 4 MIT 1 4 1 Updated Feb 19, 2026
  • CDR-Finder Public Forked from EichlerLab/CDR-Finder

    Workflow to identify the centromere dip regions (CDR) from methyl BAMs. Fork for CenMAP.

    logsdon-lab/CDR-Finder’s past year of commit activity
    Python 0 3 1 0 Updated Feb 10, 2026
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