<strong>SMARTdenov</strong><strong>o: A <em>de novo</em> Assembler Using Long Noisy Reads</strong>

Abstract

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It also has been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler&amp;mdash; SMARTdenovo, which is an SMS assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a fast assembler that did not require highly accurate raw reads for error correction, unlike other, contemporaneous SMS assemblers. It has performed well for evaluating congeneric assemblers and has been successful for a variety of 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, and here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.

The complete mitochondrial and plastid genomes of Rhododendron simsii, an important parent of widely cultivated azaleas

“…All mapped reads were extracted for the following assemblies. Firstly, we used Canu v1.7 (Koren et al 2017) and SMARTdenovo v1.0.0 (https://github.com/ruanjue/smartde novo) (Liu et al 2020) to generate two primary assemblies.…”

CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

“…Six recent community-validated assemblers are currently included (Canu [5], [6], Raven [7], MiniAsm [8] (coupled with minipolish [9] for an initial polishing), Shasta [10], smartDeNovo [11]), as well as several tools for polishing (Racon [12] and Pilon [13] for ONT and PB data, Medaka [14] and Nanopolish [15] for ONT data only). If requested, Circlator [16] or a dedicated internal tool can automatically circularise the primary output of assemblers that cannot handle circular molecules (see Supplementary information part 2.2 for more details).…”

“…Six recent community-validated assemblers are currently included (Canu [5], Flye [6], Raven [7], MiniAsm [8] (coupled with minipolish [9] for an initial polishing), Shasta [10] and smartDeNovo [11]). Several tools for polishing (Racon [12], Pilon [13], Medaka [14] and Nanopolish [15]) were also included.…”

A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data

“…The D. huoshanense genome was assembled using PacBio long-read sequencing data, followed by the integration of Illumina paired-end data and Hi-C sequencing data. First, the PacBio sequencing data were de novo assembled into contigs using smartdenovo ( Liu et al. 2020 ) after a correction process with Canu ( Koren et al.…”