Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed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

How to cite: Liu, H.; Wu, S.; Li, A.; Ruan, J. SMARTdenovo: A de novo Assembler Using Long Noisy Reads. Preprints 2020, 2020090207 (doi: 10.20944/preprints202009.0207.v1). Liu, H.; Wu, S.; Li, A.; Ruan, J. SMARTdenovo: A de novo Assembler Using Long Noisy Reads. Preprints 2020, 2020090207 (doi: 10.20944/preprints202009.0207.v1).

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— 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.

Subject Areas

SMARTdenovo; single-molecule sequencing; genome assembly

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