RT Journal
A1 Yu, Wenjuan
A1 Luo, Haohui
A1 Yang, Jinbao
A1 Zhang, Shengchen
A1 Jiang, Heling
A1 Zhao, Xianjia
A1 Hui, Xingqi
A1 Sun, Da
A1 Li, Liang
A1 Wei, Xiu-qing
A1 Lonardi, Stefano
A1 Pan, Weihua
T1 Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
JF Genome Research 
JO Genome Research 
YR 2024 
FD February 01 
VO 34 
IS 2 
SP 326 
OP 340 
DO 10.1101/gr.278232.123 
UL http://genome.cshlp.org/content/34/2/326.abstract 
AB Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic data sets with different ploidy, sequencing coverage levels, heterozygosity rates, and sequencing error rates; (3) one real metagenomic data set; and (4) five synthetic metagenomic data sets with different composition abundance and heterozygosity rates. The 11 assemblers were evaluated using quality assessment tool (QUAST) and benchmarking universal single-copy ortholog (BUSCO). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time, and memory utilization. Results show that hifiasm and hifiasm-meta should be the first choice for assembling eukaryotic genomes and metagenomes with HiFi data. We performed a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.