An efficient error correction and accurate assembly tool for noisy long reads

Abstract

Long read sequencing data, particularly those derived from the Oxford Nanopore (ONT) sequencing platform, tend to exhibit a high error rate. Here, we present NextDenovo, a highly efficient error correction and assembly tool for noisy long reads, which achieves a high level of accuracy in genome assembly. NextDenovo can rapidly correct reads; these corrected reads contain fewer errors than other comparable tools and are characterized by fewer chimeric alignments. We applied NextDenovo to the assembly of high quality reference genomes of 35 diverse humans from across the world using ONT Nanopore long read sequencing data. Based on these de novo genome assemblies, we were able to identify the landscape of segmental duplications and gene copy number variation in the modern human population. The use of the NextDenovo program should pave the way for population-scale long-read assembly, thereby facilitating the construction of human pan-genomes, using Nanopore long read sequencing data.

A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max

“…1) Draft assembly. At first, three set of contigs were independently produced by various assemblers, i.e., Hifiasm 29, 30 , NextDenovo 31 and Canu 32 . Both of Hifiasm and NextDenovo used all the PacBio Hifi and ONT ultralong reads, and Canu used PacBio reads only.…”

“…The PacBio Hifi reads were input to Hifiasm 29 (version: 0.19.5-r590, default parameters) to generate a Hifi graph, and the ONT ultralong reads were then aligned to the graph to produce choromosome-level contigs 30 . For NextDenovo 31 (version: 2.5.2, parameters: read_cutoff = 1k, genome_size = 1g), the ONT ultralong reads were input at first to produce initial contigs which were further polished by NextPolish 51 (version: 1.4.1, parameters: -x map-hifi -min_read_len 1k -max_depth 100) with input PacBio Hifi reads. For Canu 32 (version: 2.2, parameters: genomeSize=1g), only the PacBio Hifi reads were input to produce Hifi-only contigs.…”

Reinstatement of the fission yeast species Schizosaccharomyces versatilis Wickerham et Duprat, a sibling species of Schizosaccharomyces japonicus

“…We employed nextdenovo v2.5.0 (https://github.com/Nextomics/ NextDenovo) to perform de novo assembly using Oxford Nanopore reads longer than 200 kb (about 211× coverage based on a genome size of 12 Mb) (Hu, Wang, Sun, et al, 2023) (Figure S1a). A total of four contigs were produced with a combined length of 15,372,310 bp.…”

A centromere map based on super pan‐genome highlights the structure and function of rice centromeres

“…We de novo assembled 19 African rice genomes using Nanopore long reads with quality larger than seven using NextDenovo (Hu et al, 2023) (version 2.4; parameter "genome size = 370 Mb, read cutoff = 50,000, seed cutoff = 56,000, and seed depth = 45"), and raw contigs were polished three times with Nanopore long reads and Illumina short reads using NextPolish (version 1.4.1) (Hu et al, 2020) with default parameters. Illumina short reads were then aligned to each assembly with BWA (version 0.7.17-r1188) (Li and Durbin, 2009).…”