Repositories list

• compteam_tools

  Public
  A collection of custom scripts for everyday long read analysis

  Python

  •1•0•0•0•Updated Oct 9, 2025Oct 9, 2025

• ntsm_smk

  Public
  Snakemake pipeline for running ntsm to check sample contaminations

  mupad

  •0•0•0•0•Updated Oct 8, 2025Oct 8, 2025

• docker_hub

  Public
  Repository for Testing Automatic Builds with Docker Hub

  Python

  •1•1•0•0•Updated Oct 8, 2025Oct 8, 2025

• assembly_qc

  Public
  assembly QC pipeline starts with foreign contamination screening

  Python

  •1•0•0•0•Updated Oct 2, 2025Oct 2, 2025

• hifiasm-smk

  Public
  Snakemake software repo for hifiasm

  Python

  •

  MIT License

  •0•1•0•0•Updated Sep 15, 2025Sep 15, 2025

• basecall_dorado

  Public
  Snakemake repository for basecalling with dorado

  Python

  •0•0•0•0•Updated Sep 5, 2025Sep 5, 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

• assembly_eval

  Public
  Python

  •1•3•0•0•Updated Aug 22, 2025Aug 22, 2025

• reads_processing

  Public
  Support for quality trimming and downsampling from the longest reads for reads used in assembly construction.

  Python

  •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

• asap

  Public
  Autism Susceptibility Analysis Pipeline with focus in Structural Variants

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

• align_all

  Public
  A general read-alignment pipeline for PacBioHiFi, ONT, and Illumina data.

  Python

  •0•0•0•0•Updated Aug 5, 2025Aug 5, 2025

• svpop

  Public
  Variant annotation and merging pipeline

  Python

  •8•39•4•0•Updated Jul 22, 2025Jul 22, 2025

• back-reference-qc

  Public
  Detect outlier long-reads by using its Illumina counterpart.

  Python

  •2•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•9•0•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

  •9•126•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

• dss-snakemake

  Public
  A Snakemake pipeline for differential methylation analysis using DSS

  Python

  •0•1•0•0•Updated Jan 26, 2024Jan 26, 2024

• subseq-smk

  Public
  Snakemake pipeline which leverages subseq to validate structural variants

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 25, 2023Oct 25, 2023

• ont_stats

  Public
  Pipeline for getting sequencing statistics from ONT FASTQs

  Python

  •0•1•0•0•Updated Oct 13, 2023Oct 13, 2023