ILoci: robust evaluation of genome content and organization for provisional and mature genome assemblies.

ABSTRACT: We introduce a new framework for genome analyses based on parsing an annotated genome assembly into distinct interval loci (iLoci), available as open-source software as part of the AEGeAn Toolkit (https://github.com/BrendelGroup/AEGeAn). We demonstrate that iLoci provide an alternative coordinate system that is robust to changes in assembly and annotation versions and facilitates granular quality control of genome data. We discuss how statistics computed on iLoci reflect various characteristics of genome content and organization and illustrate how these statistics can be used to establish a baseline for assessment of the completeness and accuracy of the data. We also introduce a well-defined measure of relative genome compactness and compute other iLocus statistics that reveal genome-wide

SUBMITTER: Standage DS 

PROVIDER: S-EPMC8862717 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature