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Popup Demo: Getting started with snakemake for workflow automation in bioinformatics
January 20, 2021 @ 2:00 pm - 4:00 pm
REGISTRATION
No registration required. Tune in to https://www.twitch.tv/ctitusbrown to watch.
DESCRIPTION
Practical bioinformatics often involves processing dozens to 100s of samples with command line tools. Snakemake is an automation and workflow system that lets you coordinate and execute workflows; it natively supports most HPC systems as well. I’ll start with a standard set of variant calling commands, and walk through tying them together into a fully automated and scalable snakemake workflow.
PREREQUISITES
None.
SPEAKER
Professor Brown serves as DataLab’s Director of Community Initiatives. The Brown lab focuses on genomic, transcriptomic, and metagenomic sequence analysis. The lab is the primary developer of the khmer software, for faster and more efficient sequence analysis of high-throughput sequencing data. They also run quite a bit of training in data-intensive biology. Professor Brown serves on DataLab recruitment committees, teaches workshops, leads hackathons, and participates in our strategic activities and planning. His lab also runs the “Meet and Analyze (biological) Data” (aka MAD) weekly drop-in office hours.