Chloroplast genome assembly approaches from NGS data

Authors

  • 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.

Downloads

Published

2017-07-11

Issue

Vol. 5 No. 3 (2016)

Section

Bioinformatics

License

Authors of articles published in Journal of BioScience and Biotechnology retain the copyright of their articles. The journal/publisher is not responsible for subsequent uses of the work. It is the author's responsibility to bring an infringement action if so desired by the author.

Authors retain the following rights:
  • copyright, and other proprietary rights relating to the article, such as patent rights;
  • the right to use the substance of the article in future own works, including lectures and books;
  • the right to reproduce the article for own purposes, provided the copies are not offered for sale;
  • the right to self-archive the article.