Utilities for analyzing next generation sequencing data.
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Updated
May 7, 2021 - Shell
Utilities for analyzing next generation sequencing data.
Pipelines to run STRUCTURE using multiple front-ends (CLUMPAK+StrAuto, Structure_threader)
A probably over-engineered bash-script for starting parallel runs of structure for different population sizes and numbers of replicates.
GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.
Scripts and notes related to the manuscript: Stuart KC & Cardilini APA 2021 Signatures of selection in a recent invasion reveal adaptive divergence in a highly vagile invasive species. Molecular Ecology 30(6):1419-1434, doi.org/10.1111/mec.15601 † joint first author ‡ joint last author.
Set of scripts to run STRUCTURE in parallel on computing grids like MetaCentrum. Scripts are designed for grids and clusters using PBS Pro, but can be easily adopted for another queue system.
A protocol for applying low-coverage whole-genome sequencing data in structure variation studies
A Docker repository for a course on analysis of genomic data
Pipelines to identify polymorphic genetic and methylation variants
Set of scripts used for the paper "A Neurodegenerative Disease Landscape of Rare Mutations in Colombia Due to Founder Effects"
Code accompanying the manuscript on Genome variation in alpine bumblebees.
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