Low Wai Yee

Invited Talk Title:

To snake or to flow: comparison of Snakemake and Nextflow

Abstract:

Computational pipelines are integral in bioinformatics, particularly for high-throughput sequenced data. While traditional Shell scripting is a common method, alternatives like Snakemake and Nextflow have gained popularity. Notably, the verkko assembler for assembling complete human telomere-to-telomere genomes uses a Snakemake pipeline. This workshop addresses common queries such as the choice between Shell scripting and workflow management systems like Snakemake or Nextflow. By demonstrating variant calling with both Shell scripts and these systems, the workshop provides insights into factors to consider, including scalability. Pros and cons of each method underscore the idea that the optimal approach depends on specific task requirements and features.