Comprehensive Assessment of Elevende novoHiFi Assemblers on Complex Eukaryotic Genomes and Metagenomes

Abstract

Background: Pacific Bioscience HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (less than 0.01% sequencing error). While several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. Results: We evaluated the performance of eleven de novo HiFi assemblers on (i) real data for three eukaryotic genomes, (ii) 34 synthetic datasets with different ploidy, sequencing coverage levels, heterozygosity rates and sequencing error rates, (iii) one real metagenomic dataset, and (iv) five synthetic metagenomic datasets with different composition abundance and heterozygosity rates. The nine assemblers were evaluated using QUAST (Quality Assessment Tool) and BUSCO (Benchmarking Universal Single-Copy Ortholog). 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. On complex eukaryotic genomes, Hifiasm had a clear advantage over the other assemblers in all tested experiments. On synthetic datasets, Hifiasm, HiCanu, and HiFlye performed equally well. Shasta and Peregrine had good performance across varying ploidy, but required high computational resources. On metagenomic datasets, Hifiasm-meta demonstrated a clear advantage over other assemblers. Conclusion: We carried out 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.

Pre-Assembly NGS Correction of ONT Reads Achieves HiFi-Level Assembly Quality

“…In summary, ONT-based tools are worse with NG50 and QV, but better with contig count, misassemblies and mismatches, and have similar or slightly worse k-mer-based completeness and indel statistics than corrected HiFi-based methods. R9 ONT UL is more expensive than R9 ONT and is usually used only to assemble up to T2T completeness in combination with other sequencing platforms such as HiFi [4,30]. Nevertheless, no assembly tool in this study can achieve T2T completeness even with 50X coverage (Supplementary Figures 3-9).…”

Comparison of Hi-C-Based Scaffolding Tools on Plant Genomes

“…A complete genome assembly should encompass all chromosomes, genes, non-coding regions, and other indispensable genomic structures and elements inherent to the organism. To evaluate the integrity and accuracy of the final assembly results, we employed various metrics rooted in unique k-mers, as defined in [14]. These metrics encompass the Complete Rate (CR), the average proportion of the largest category (PLC), and the average distance difference (ADF).…”

Phasing or purging: tackling the genome assembly of a highly heterozygous animal species in the era of high-accuracy long reads

“…The output reads are now deemed sufficient for de novo assembly without the need of additional data for polishing, which was crucial for R9. 4 Nanopore reads, and their length can still reach values over 100 kb and even 1 Megabase (Mb) [3]. In response, assembly tools have been developed or adapted to benefit from the improved accuracy of these long reads [4].…”

“…4 Nanopore reads, and their length can still reach values over 100 kb and even 1 Megabase (Mb) [3]. In response, assembly tools have been developed or adapted to benefit from the improved accuracy of these long reads [4].…”