Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes

• DOI: 10.1101/gr.278232.123
• Publication Date: 2024-03-01T15:25:26Z
• Authors: Wenjuan Yu; Haohui Luo; Jinbao Yang; Shengchen Zhang; Heling Jiang; Xianjia Zhao; Xingqi Hui; Da Sun; Liang Li; Xiu-qing Wei; Stefano Lonardi; Weihua Pan
• Keywords: Bioinformatics; Bioinformatics and Computational Biology; Genetics; Metagenome; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; Metagenomics; Biological Sciences; Medical and Health Sciences; Resources; Software; Algorithms

Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% error). Although several de novo assembly tools are available for reads, there no comprehensive studies on the evaluation of these assemblers. We evaluated performance 11 assemblers (1) real data three eukaryotic genomes; (2) 34 synthetic sets different ploidy, coverage levels, heterozygosity rates, and error rates; (3) one metagenomic set; (4) five composition abundance rates. The were using quality assessment tool (QUAST) benchmarking universal single-copy ortholog (BUSCO). also used additional criteria, namely, completion rate, duplicated average proportion largest category, distance difference, value, run-time, memory utilization. Results show that hifiasm hifiasm-meta should be first choice assembling genomes metagenomes data. performed a study commonly complex metagenomes. Our will help research community to choose most appropriate assembler their identify possible improvements in algorithms.