SMARTdenovo: a de novo assembler using long noisy reads

Abstract

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It has also been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler SMARTdenovo, a single-molecule sequencing (SMS) assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a rapid assembler, which, unlike contemporaneous SMS assemblers, does not require highly accurate raw reads for error correction. It has performed well in the evaluation of congeneric assemblers and has been successfully users for various assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015; here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.

Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

“…The last was composed of 30× of the highest-scoring Filtlong [ 31 ] reads. Then, we launched Smartdenovo [ 32 ] (git commit 8488de9), Wtdbg2/Redbean [ 33 ] (git commit b77c565), and Flye [ 34 ] (version 2.8.3) on all sets. In addition, Necat [ 35 ] (git commit d377878) was launched with the complete readset, as it corrects reads given as input and applies its own downsampling algorithm.…”

Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees

“…64 The corrected reads were assembled using SMARTdenovo. 65 The error correction of contigs was performed using Racon 66 and was iterated three times based on Nanopore reads, followed by two rounds of polishing using NextPolish 67 with Illumina short reads. With the Hi-C library, the error-corrected contigs were anchored to eight superscaffolds using the 3D-DNA pipeline 68 and juicer.…”

Exploring the evolutionary process of alkannin/shikonin O-acyltransferases by a reliable Lithospermum erythrorhizon genome

“…PacBio and ONT clean data were first corrected via NextDenovo v2.3.1 (key parameter: read_cutoff = 1,000; seed_cutoff = 10,000) ( https://github.com/Nextomics/NextDenovo ), separately. The total corrected data were then applied for genome assembly using NextDenovo v2.3.1 (key parameter: nextgraph_options = –a 1), SmartDenovo v1.0.0 28 (key parameter: –J 5000; –k 16), Flye v2.8.1 29 (key parameter: –i 1), and Wtdbg v2.5 30 (key parameter: –L 5000; –k 15; –p 0; –S 2), independently. Finally, the NextDenovo-assembled version was further polished three rounds via Pilon v1.23 31 based on Illumina clean data.…”