NOVOPlasty: de novo assembly of organelle genomes from whole genome data

By Nicolas Dierckxsens, P. Mardulyn, Guillaume Smits. Nucleic Acids Research, 2016

3,105 citations recorded by the source corpus.

Abstract The evolution in next-generation sequencing (NGS) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. These genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in GenBank. Producing organelle genome assembly from whole genome sequencing (WGS) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacking. We developed a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing (WGS) data, starting from a related or distant single seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina data sets where it outperforms known assemblers in assembly accuracy and coverage. In our benchmark, NOVOPlasty assembled all tested circular genomes in less than 30 min with a maximum memory requirement of 16 GB and an accuracy over 99.99%. In conclusion, NOVOPlasty is the sole de novo assembler that provides a fast and straightforward extraction of the extranuclear genomes from WGS data in one circular high quality contig. The software is open source and can be downloaded at https://github.com/ndierckx/NOVOPlasty.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/2f095d1fa575ea40329921a35feea7433e3fd31a

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In Genetics

1. Jun Wen
2. Z. Nie
3. Bin‐Bin Liu
4. YU-BING Wang
5. Fanglin Chen
6. Jun-bo Yang
7. Wen-bin Yu
8. Yiyuan Li

In Molecular Biology

1. Jun Wen
2. Z. Nie
3. Bin‐Bin Liu
4. YU-BING Wang
5. Fanglin Chen
6. Claude W. dePamphilis
7. Jun-bo Yang
8. Wen-bin Yu

In Plant Science

1. Z. Nie
2. Jun Wen
3. V. Funk

Citations in the corpus

• GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes (2018, methodology): “4.7, and NOVOPlasty 2.7.2 [23].”
• MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization (2019, methodology): “The two frequently-used mitogenome assembly software,MITObim (25) andNOVOPlasty (26), require closelyrelated mitochondrial fragments as seeds to anchor short reads and build initial datasets.”
• Major clades and a revised classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genome skimming (2020, methodology): “6 (Dierckxsens et al., 2016) for plastome assembly using the trimmed paired‐end reads.”