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SMARTdenovo: A de novo Assembler Using Long Noisy Reads
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: 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 https://doi.org/10.46471/gigabyte.15 Hailin Liu ,Shigang Wu ,Alun Li ,Jue Ruan ,SMARTdenovo: a de novo assembler using long noisy reads,Gigabyte,2021 https://doi.org/10.46471/gigabyte.15
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.
Keywords
SMARTdenovo; single-molecule sequencing; genome assembly
Subject
Biology and Life Sciences, Biology and Biotechnology
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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