https://github.com/pdimens/harpy

Process linked-read data, from raw sequences to phased haplotypes, batteries included. Works with WGS too!

bioinformatics haplotype linked-reads pipeline sequencing variant-calling

Last synced: 03 Feb 2026

https://github.com/pdimens/lepwrap

A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.

bioinformatics genome-assembly linkage linkage-mapping snakemake

Last synced: 20 Sep 2025

https://github.com/pdimens/bio-bin

Handy reusable bioinformatic scripts

bioinformatics fasta genome-analysis genomics julia

Last synced: 11 Apr 2025

https://github.com/pdimens/popgensims.jl

Create population genetics simulations

breeding crosses genetics mating popgen simulation

Last synced: 15 Apr 2025

https://github.com/pdimens/afsworkshop2024

Materials for the AFS2024 Workshop: Communicating Research with Effective Data Visualization & Effective Storytelling

Last synced: 05 Oct 2025

https://github.com/pdimens/haplotagging_simulations

Contains the code associated with the simulation study

Last synced: 01 Jul 2025

https://github.com/pdimens/mimick

Linked-read sequence simulator

fastq genomics genomics-data genomics-simulations linked-reads

Last synced: 08 Jun 2026

https://github.com/pdimens/c.acronotus-data-2019

SNP dataset associated with Dimens et al. 2019 "A genomic assessment of movement and gene flow around the South Florida vicariance zone in the migratory coastal blacknose shark, Carcharhinus acronotus"

Last synced: 18 Oct 2025

https://github.com/pdimens/2022-tatlanticus_popgen

Repository associated with the publication: Weak range-wide population structure in the blackfin tuna (Thunnus atlanticus) revealed by analysis of genome-wide SNPs

population-genetics

Last synced: 18 Oct 2025

https://github.com/pdimens/time-series-shad

Project repository for the American Shad genomic time series project

Last synced: 29 Jun 2026

https://github.com/pdimens/gust

An easy breezy whole-genome derived snp-based phylogenetic pipeline 🌪️

Last synced: 22 Jul 2025

https://github.com/pdimens/pdimens.github.io

Last synced: 07 Jan 2026

https://github.com/pdimens/2025-tablacares_popgen

Last synced: 02 Jan 2026

https://github.com/pdimens/brcapps

Last synced: 04 Sep 2025

https://github.com/pdimens/therksite

Last synced: 07 Jan 2026

https://github.com/pdimens/djinn

Convert linked-read FASTQ/BAM files between formats, almost like magic.

Last synced: 05 Mar 2026

https://github.com/pdimens/shortle

A Pretty Ok Short-Read Assembly Workflow

Last synced: 28 Jul 2026