Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

SMARTdenovo: A de novo Assembler Using Long Noisy Reads

Version 1 : Received: 7 September 2020 / Approved: 9 September 2020 / Online: 9 September 2020 (10:48:24 CEST)

A peer-reviewed article of this Preprint also exists.

Hailin Liu ,Shigang Wu ,Alun Li ,Jue Ruan ,SMARTdenovo: a de novo assembler using long noisy reads,Gigabyte,2021 Hailin Liu ,Shigang Wu ,Alun Li ,Jue Ruan ,SMARTdenovo: a de novo assembler using long noisy reads,Gigabyte,2021


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— 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.


SMARTdenovo; single-molecule sequencing; genome assembly


Biology and Life Sciences, Biology and Biotechnology

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