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    84 repositories

    • align_all

      Public
      A general read-alignment pipeline for PacBioHiFi, ONT, and Illumina data.
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 21, 2026Apr 21, 2026

    • docker_hub

      Public
      Repository for Automated Docker Builds with Docker Hub
      Python
      •0•1•0•0•Updated Apr 21, 2026Apr 21, 2026

    • compteam_tools

      Public
      A collection of custom scripts for everyday long read analysis
      Python
      •0•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • basecall_dorado

      Public
      Snakemake repository for basecalling with dorado
      Python
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • asap

      Public
      Autism Susceptibility Analysis Pipeline with focus in Structural Variants
      Python
      •
      MIT License
      •1•2•0•0•Updated Apr 17, 2026Apr 17, 2026

    • Rhodonite_eichler

      Public
      Perl
      •
      MIT License
      •0•0•0•0•Updated Apr 3, 2026Apr 3, 2026

    • sedef_smk

      Public
      A snakemake pipeline for SEDEF.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 27, 2026Mar 27, 2026

    • assembly_qc

      Public
      assembly QC pipeline starts with foreign contamination screening
      Python
      •1•1•0•0•Updated Mar 24, 2026Mar 24, 2026

    • sample-id-check

      Public
      Snakemake pipeline for running ntsm to check sample contaminations
      Python
      •0•0•0•0•Updated Mar 17, 2026Mar 17, 2026

    • assembly_eval

      Public
      Python
      •0•3•0•0•Updated Mar 3, 2026Mar 3, 2026

    • long_read_downsampling

      Public
      Support for quality trimming and downsampling from the longest reads for reads used in assembly construction.
      Python
      •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • subseq-smk

      Public
      Snakemake pipeline which leverages subseq to validate structural variants
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 5, 2026Jan 5, 2026

    • hifiasm-smk

      Public
      Snakemake software repo for hifiasm
      Python
      •
      MIT License
      •0•1•0•0•Updated Dec 23, 2025Dec 23, 2025

    • AoU_WDL

      Public
      Repository for storing WDL workflows for execution in the AoU Researcher Workbench
      WDL
      •1•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • svpop

      Public
      Variant annotation and merging pipeline
      Python
      •8•43•4•0•Updated Jul 22, 2025Jul 22, 2025

    • back-reference-qc

      Public
      Detect outlier long-reads by using its Illumina counterpart.
      Python
      •1•0•0•0•Updated Jun 13, 2025Jun 13, 2025

    • CDR-Finder

      Public
      Workflow to identify the centromere dip regions (CDR) from methyl BAMs
      Python
      •3•14•1•0•Updated Jun 4, 2025Jun 4, 2025

    • snakemake_pipelines

      Public
      General Snakemake pipelines.
      Python
      •0•0•0•0•Updated Feb 28, 2025Feb 28, 2025

    • audano_curve

      Public
      Python
      •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • pav

      Public
      Phased assembly variant caller
      Python
      •10•139•9•0•Updated Dec 4, 2024Dec 4, 2024

    • data_table

      Public
      Variant and annotation integration
      Python
      •0•0•0•0•Updated Jul 17, 2024Jul 17, 2024

    • read_depth_genotyper

      Public
      Get genotypes for regions using WSSD and SUNK
      Python
      •2•1•0•1•Updated Jul 11, 2024Jul 11, 2024

    • CDR-Finder_smk

      Public
      CDR-Finder
      Python
      •3•0•0•0•Updated May 24, 2024May 24, 2024

    • reassign-sex-chr

      Public
      Pipeline for reassigning duplicated or fragmented sex chromosomes to isolated haplotypes
      Python
      •0•0•0•0•Updated May 9, 2024May 9, 2024

    • denovo_sv_validation

      Public
      Pipeline for validation of de novo SVs
      Python
      •
      MIT License
      •3•2•0•0•Updated Apr 23, 2024Apr 23, 2024

    • subseq

      Public
      Pipeline for validating variant calls with support from individual reads
      C++
      •
      MIT License
      •1•1•0•0•Updated Apr 11, 2024Apr 11, 2024

    • fastCN-smk

      Public
      Python
      •
      MIT License
      •4•0•0•0•Updated Feb 28, 2024Feb 28, 2024

    • long-reads-public-codebase

      Public
      This Repo will be for the sharing of code for the long reads analysis initiative.
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Feb 20, 2024Feb 20, 2024

    • ONT_pipelines

      Public
      Python
      •
      MIT License
      •2•3•0•0•Updated Feb 13, 2024Feb 13, 2024

    • continuous-methylation

      Public
      A Snakemake pipeline for methylation analysis using long-read sequencing (third generation).
      Python
      •1•0•0•0•Updated Jan 29, 2024Jan 29, 2024
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