Pay Giesselmann from the Max Planck Institute for Molecular Genetics in Germany presented at London Calling 2019 on “Nanopype: processing and quantification of short tandem repeats.” The team created a data processing pipeline for targeted repeat expansion analysis and worked on STRique to quantify repeat expansion. Nanopype can be installed from the source, used as an all-in-one Docker container, or available as Singularity images per module. Nanopype works on batches of reads, explained Giesselmann. The methylation workflow can be started with Snakemake and a single line of code. Tracks of methylation can be created. For short tandem repeats, STRique can count repeats and determine their length. Giesselmann shared an application: sequencing of a patient with a repeat expansion. The patient had two groups of 400 and 780 repeats. Methylation detection was applied to another case that helped identify the methylation state of the repeat itself. Gisselmann concluded that their pipelines enable an analysis of repeat expansion applied to patient samples. I am always impressed with how much data can be mined from sequencing output!
