Software

Software Tools

The following software tools were developed and used in GrENE-net, but you can also use them in your research!

grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with support for both individual samples and pool sequencing. It provides a comprehensive workflow for read trimming, mapping, variant calling, and quality control.

grenedalf

A toolkit for population genetic statistics from pool-sequenced samples, specifically designed for evolve and resequence experiments. It provides efficient implementations of various population genetic statistics and analyses.

HapFIRE

A tool for haplotype-based inference of recombination events, designed to work with pool-sequencing data. It helps in understanding recombination patterns and their impact on genetic diversity.

Note: All tools are open-source and available, we welcome contributions and feedback from the community.