Abstract
We developed grenepipe, an all-in-one Snakemake workflow to streamline the data processing from raw high-throughput sequencing data of individuals or populations to genotype variant calls. Our pipeline offers a range of popular software tools within a single configuration file, automatically installs software dependencies, is highly optimized for scalability in cluster environments and runs with a single command. grenepipe is published under the GPLv3 and freely available at github.com/moiexpositoalonsolab/grenepipe.
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