gcaPDA: a haplotype-resolved diploid assembler

BMC Bioinformatics

Mingzhi Ye¹  Tianquan Deng¹  Xin Yang¹  Lijuan He¹  Shixuan Chen¹  Min Xie¹  Shenshen Wu²  Jianbing Yan²  Linfeng Yang²  Chenglin Jiang²  Cheng Luo²  Ning Yang² 

[1] Guangdong Engineering Research Center of Plant and Animal Genomics, BGI Genomics, BGI-Shenzhen;National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University;

关键词: Haplotype-resolved de novo assembler;    Diploid;    Highly heterozygous genomes;    Gamete cells;   

DOI  :  10.1186/s12859-022-04591-4

来源: DOAJ

【 摘 要 】

Abstract Background Generating chromosome-scale haplotype resolved assembly is important for functional studies. However, current de novo assemblers are either haploid assemblers that discard allelic information, or diploid assemblers that can only tackle genomes of low complexity. Results Here, Using robust programs, we build a diploid genome assembly pipeline called gcaPDA (gamete cells assisted Phased Diploid Assembler), which exploits haploid gamete cells to assist in resolving haplotypes. We demonstrate the effectiveness of gcaPDA based on simulated HiFi reads of maize genome which is highly heterozygous and repetitive, and real data from rice. Conclusions With applicability of coping with complex genomes and fewer restrictions on application than most of diploid assemblers, gcaPDA is likely to find broad applications in studies of eukaryotic genomes.

【 授权许可】

Unknown