Chloroplast genome assembly approaches from NGS data

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.

Keywords

• Next-generation sequencing
• Genome assembly
• assembly algorithms
• chloroplast genome