JCVI: A versatile toolkit for comparative genomics analysis

• DOI: 10.1002/imt2.211
• Publication Date: 2024-06-13T06:14:03Z
• Authors: Haibao Tang; Vivek Krishnakumar; Xiaofei Zeng; Zhougeng Xu; Adam Taranto; Johnathan S. Lomas; Yixing Zhang; Yumin Huang; Yibin Wang; Won Cheol Yim; Jisen Zhang; Xingtan Zhang
• Keywords: 0301 basic medicine; 03 medical and health sciences; genome annotation; Computer applications to medicine. Medical informatics; genome assembly; R858-859.7; Method; comparative genomics; genomic data; visualization

AbstractThe life cycle of genome builds spans interlocking pillars of assembly, annotation, and comparative genomics to drive biological insights. While tools exist to address each pillar separately, there is a growing need for tools to integrate different pillars of a genome project holistically. For example, comparative approaches can provide quality control of assembly or annotation; genome assembly, in turn, can help to identify artifacts that may complicate the interpretation of genome comparisons. The JCVI library is a versatile Python‐based library that offers a suite of tools that excel across these pillars. Featuring a modular design, the JCVI library provides high‐level utilities for tasks such as format parsing, graphics generation, and manipulation of genome assemblies and annotations. Supporting genomics algorithms like MCscan and ALLMAPS are widely employed in building genome releases, producing publication‐ready figures for quality assessment and evolutionary inference. Developed and maintained collaboratively, the JCVI library emphasizes quality and reusability.