Datensatz

Zusammenfassung

Long-read third-generation nanopore sequencing enables researchers to now address a
range of questions that are difficult to tackle with short read approaches. The rapidly expanding
user base and continuously increasing throughput have sparked the development of a growing
number of specialized analysis tools. However, streamlined processing of nanopore datasets using
reproducible and transparent workflows is still lacking. Here we present Nanopype, a nanopore
data processing pipeline that integrates a diverse set of established bioinformatics software while
maintaining consistent and standardized output formats. Seamless integration into compute cluster
environments makes the framework suitable for high-throughput applications. As a result,
Nanopype facilitates comparability of nanopore data analysis workflows and thereby should enhance
the reproducibility of biological insights.