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Article|01 Aug 2022|OPEN
RAviz: a visualization tool for detecting false-positive alignments in repetitive genomic regions
Dong Xu1 ,† , Yu Song1,2 ,† , Xianjia Zhao1,2 and Desheng Gong1 , Yingxue Yang1 , , Weihua Pan,1 ,
1Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
2Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan Zhengzhou 450001, China
*Corresponding author. E-mail: yangyingxue@caas.cn,panweihua@caas.cn
Both authors contributed equally to the study.

Horticulture Research 9,
Article number: uhac161 (2022)
doi: https://doi.org/10.1093/hr/uhac161
Views: 75

Received: 20 May 2022
Accepted: 08 Jul 2022
Published online: 01 Aug 2022

Abstract

Dear Editor,

For any species, a high-quality reference genome is the basis for almost all kinds of genomic analysis [1]. However, for decades the reference sequences of important eukaryotic genomes were incomplete due to the missing repetitive genomic regions including both tandem repeats such as centromere, telomere, and ribosomal DNA, and interspersed repeats like transposons and segmental duplications. The incomplete reference genomes not only cause data analytical mistakes like false-positive variant calls but also impede the studies of repeat-related diseases such as cancer and infertility [23]. Fortunately, the generation of Pacbio high-fidelity (HiFi) long sequences and Oxford Nanopore Technology (ONT) ultra-long (UL) sequences provides the opportunity of solving repeat assembly problems because of their advantages in accuracy and length, respectively, and a list of complete (T2T, or Telomere to Telomere) or near-complete reference genomes of important eukaryotic species like human [4], Arabidopsis [5], rice [6] and tomato [7] have been built recently.