Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs.

ABSTRACT: The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g. genes) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpy's utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by

SUBMITTER: Madrigal G 

PROVIDER: S-EPMC11646305 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature