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Updated: Aug 30, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads
Lucas Czech1, Moises Exposito-Alonso1,2,3
1Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
Summary:
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.
Availability And Implementation:
grenepipe is published under the GPLv3 and freely available at github.com/moiexpositoalonsolab/grenepipe.
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