Chloroplast genome assembly approaches from NGS data

  • Zdravka Petrova Ivanova University of Plovdiv "Paisii Hilendarski", Department of Plant Physiology and Molecular Biology, 24 Tzar Asen Str., Plovdiv 4000, Bulgaria
  • Evelina Daskalova University of Plovdiv "Paisii Hilendarski", Department of Plant Physiology and Molecular Biology, 24 Tzar Asen Str., Plovdiv 4000, Bulgaria.
  • Georgi Minkov University of Plovdiv "Paisii Hilendarski", Department of Plant Physiology and Molecular Biology, 24 Tzar Asen Str., Plovdiv 4000, Bulgaria.
  • Vesselin Baev University of Plovdiv "Paisii Hilendarski", Department of Plant Physiology and Molecular Biology, 24 Tzar Asen Str., Plovdiv 4000, Bulgaria.

Abstract

The advent of Next Generation Sequencing platforms led to increase of research in whole genome assembly algorithms and software. Illumina Genome Analyzer produces a large amount of sequencing data, with a shorted read length, higher coverage and different errors in comparison to Sanger Sequencing. In response to this, several new assemblers were developed specifically for de novo assembly of next generation sequencing. This study compares software assembly packages named Edena, SPAdes, ABySS and analyzes results delivered by de novo assembly experiments. We show that assembly job of small genome can be completed in a short time on a 32 bit Linux OS with 4 GB RAM, indicating than de novo assembly can be executed and millions of very reads assembled on a desktop computer.

Published
2017-07-11
Section
Bioinformatics