Chloroplast genome assembly approaches from NGS data
Journal Title: Journal of BioScience and Biotechnology - Year 2016, Vol 5, Issue 3
Abstract
The advent of Next Generation Sequencing platforms has led to significant research innovation in the field of whole genome assembly algorithms and software. The Illumina platforms produce large amounts of distinctive sequencing data with a shorter read length and higher coverage in comparison with Sanger Sequencing. In response to this, several new assemblers were developed specifically for de novo assembly of next generation sequencing data. This study compares software assembly packages named Edena, SPAdes, ABySS and analyzes the results delivered by de novo assembly experiments. We showed that a plastid genome assembly can be completed on a 32 bit Linux OS with 4 GB RAM, indicating that an experiment including de novo chloroplast assembly of millions very short reads can be executed successfully and quickly on a desktop computer.
Authors and Affiliations
Zdravka Ivanova, Evelina Daskalova, Georgi Minkov, Vesselin Baev
Keywords
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