Repositories list

• sv_prediction

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 2, 2026Jan 2, 2026

• sudmantlab.github.io

  Public
  lab web page

  HTML

  •2•1•0•0•Updated Jan 2, 2026Jan 2, 2026

• loco-pipe

  Public
  loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data

  Python

  •

  GNU General Public License v3.0

  •5•25•6•0•Updated Jan 2, 2026Jan 2, 2026

• 17q21.31_SV_and_evolution

  Public
  Rapid turnover and recurrent structural variation at the 17q21.31 locus in modern and ancient human genomes, and primates

  Python

  •0•0•0•0•Updated Jan 2, 2026Jan 2, 2026

• vesper

  Public
  single read SV caller for PacBio HiFi data

  Python

  •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

• rishi

  Public
  0•0•0•0•Updated Oct 30, 2025Oct 30, 2025

• hifi_dn_alu

  Public
  Snakemake pipeline and documents for "Direct identification of de novo mobile element insertions from single molecule sequencing of human sperm".

  Python

  •0•0•0•0•Updated Aug 14, 2025Aug 14, 2025

• nova

  Public
  de novo insertion simulator

  Python

  •0•1•0•0•Updated Jul 1, 2025Jul 1, 2025

• amylase_diversity_project

  Public
  Python

  •2•21•2•0•Updated Dec 13, 2024Dec 13, 2024

• MyotisGenomeAssembly

  Public
  A home for our assembly pipeline for Myotis genomes using HiFi + Hi-C

  HTML

  •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

• conplastic_mt_profiling

  Public
  Jupyter Notebook

  •0•2•0•0•Updated Oct 15, 2024Oct 15, 2024

• visualization_hub

  Public
  0•0•0•0•Updated Jun 5, 2024Jun 5, 2024

• trackhubs

  Public
  0•0•0•0•Updated Jan 10, 2024Jan 10, 2024

• snakemake_workshop

  Public
  A copy of the Fall 2023 CCB Skills Seminar on snakemake, developed and taught by @stacy-l.

  Python

  •6•0•0•0•Updated Oct 16, 2023Oct 16, 2023

• rockfishgenomeproject

  Public
  HTML

  •2•6•0•0•Updated Oct 2, 2023Oct 2, 2023

• Project-AgeExpressionConstraint

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Jul 4, 2023Jul 4, 2023

• DuplexSequencingPipeline

  Public
  HTML

  •0•0•0•0•Updated Mar 6, 2023Mar 6, 2023

• ht_scripts

  Public
  Code and binaries related to processing haplotagging data

  C++

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Jan 11, 2023Jan 11, 2023

• PPRP

  Public
  0•0•0•0•Updated Oct 31, 2022Oct 31, 2022

• seqlib

  Public
  Python

  •0•0•0•0•Updated Jun 16, 2022Jun 16, 2022

• gene_expression_aging

  Public
  R

  •0•6•0•0•Updated May 17, 2022May 17, 2022

• pggb_primate_example

  Public
  Python

  •0•0•0•0•Updated May 16, 2022May 16, 2022

• greatape_cnv

  Public
  Calculating the copy number variation of the great apes.

  Jupyter Notebook

  •0•1•0•0•Updated Jul 12, 2021Jul 12, 2021

• SingYeastcDNAScreening

  Public
  Python

  •0•0•0•0•Updated May 4, 2021May 4, 2021

• ERVDist

  Public
  0•0•0•0•Updated Dec 17, 2020Dec 17, 2020

• sudmanthelp

  Public
  sudmant lab first-aid kit with useful utility functions and common issues

  Python

  •0•0•2•0•Updated Sep 18, 2019Sep 18, 2019

• gtf-to-genes

  Public
  Automatically exported from code.google.com/p/gtf-to-genes

  Python

  •1•0•0•0•Updated Jul 6, 2019Jul 6, 2019

• treemlratetest

  Public
  Python

  •0•0•0•0•Updated Jun 28, 2019Jun 28, 2019

• Duplex-Sequencing

  Public
  Python

  •

  Other

  •32•0•0•0•Updated Sep 19, 2017Sep 19, 2017

• DuplexSequencingScripts

  Public
  Python

  •2•0•0•0•Updated Dec 12, 2016Dec 12, 2016