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  • PMID: 27924028 was deleted because it is a duplicate of PMID: 28204566
Nucleic Acids Res. 2017 Feb 28;45(4):e18. doi: 10.1093/nar/gkw955.

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

Author information

1
Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles and Vrije Universiteit Brussel, Triomflaan CP 263, 1050 Brussels, Belgium.

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.

PMID:
28204566
PMCID:
PMC5389512
DOI:
10.1093/nar/gkw955
[Indexed for MEDLINE]

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