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bergen_target_capture_workshop_april2022

Scripts and results from the target capture workshop held by Martha Kandziora and Seth Musker at the University of Bergen, 26-27 April 2022

captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

construct

method for modeling continuous and discrete population genetic structure

dadi_pipeline

An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.

embarcadero

🌲🌉 BART species distribution models 🌉 🌲

gbs_snp_filter

filtering SNPs based on LD and HWE status

genocae

Convolutional autoencoder for genotype data

herbchomper_msa

A bioinformatic tool for trimming poorly-aligned ends from DNA sequences

hybpiper_phasing_phyloscripts_modified

lea

lsd

This repository contains a suite of scripts for performing LSD genome scans based on explicit demographic models (Luqman et al. 2021; https://www.biorxiv.org/content/10.1101/2020.07.20.211581v2.full.pdf)

mscquartets-parallel

personalutilities

snps2cf

An R function to compute Concordance Factors from SNP datasets

spacemix

starmie

starmie: plotting and inference for population structure models :star2:

targetsupercontigs

Phylogenomics: extract supercontigs from (draft) genome assemblies for more effective target capture sequencing

targetvet

Target Capture (aka Hyb-seq) marker vetting using WGS data.

vcf2construct

convert VCF biallelic SNP data to format required for conStruct R package (https://github.com/gbradburd/conStruct)