LocoGSE, a sequence-based genome size estimator for plants.

ABSTRACT: Extensive research has focused on exploring the range of genome sizes in eukaryotes, with a particular emphasis on land plants, where significant variability has been observed. Accurate estimation of genome size is essential for various research purposes, but existing sequence-based methods have limitations, particularly for low-coverage datasets. In this study, we introduce LocoGSE, a novel genome size estimator designed specifically for low-coverage datasets generated by genome skimming approaches. LocoGSE relies on mapping the reads on single copy consensus proteins without the need for a reference genome assembly. We calibrated LocoGSE using 430 low-coverage Angiosperm genome skimming datasets and compared its performance against other estimators. Our results demonstrate that LocoGSE a

SUBMITTER: Guenzi-Tiberi P 

PROVIDER: S-EPMC10972871 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature