JCVI: A versatile toolkit for comparative genomics analysis
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
Affiliations
Haibao Tang
Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology and College of Life Sciences Fujian Agriculture and Forestry University Fuzhou Fujian China
Vivek Krishnakumar
J. Craig Venter Institute Rockville Maryland USA
Xiaofei Zeng
National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
Zhougeng Xu
National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE) Chinese Academy of Sciences (CAS) Shanghai China
Adam Taranto
School of BioSciences The University of Melbourne Melbourne Victoria Australia
Johnathan S. Lomas
Department of Biochemistry and Molecular Biology University of Nevada Reno Nevada USA
Yixing Zhang
Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology and College of Life Sciences Fujian Agriculture and Forestry University Fuzhou Fujian China
Yumin Huang
Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology and College of Life Sciences Fujian Agriculture and Forestry University Fuzhou Fujian China
Yibin Wang
National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
Won Cheol Yim
Department of Biochemistry and Molecular Biology University of Nevada Reno Nevada USA
Jisen Zhang
State Key Lab for Conservation and Utilization of Subtropical Agro‐Biological Resources, Guangxi Key Lab for Sugarcane Biology Guangxi University Nanning Guangxi China
Xingtan Zhang
National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
Abstract The 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.
