Short read de novo analysis

Applied Biosystems has expanded its suite of bioinformatics solutions to include de novo assembly of small organisms on the Solid 3 System, the company’s sequencing platform that enables the comprehensive analysis of genomes, transcriptomes and epigenomes. Two analysis tools from SoftGenetics and the European Bioinformatics Institute (EBI) were developed to help researchers reconstruct, assemble and visualise short-read sequencing data generated by the Solid technology.

Enhancements to the Solid 3 System, including faster run times, longer read lengths and the incorporation of an imaging buffer that improves signal-to-noise ratio, make the platform suitable for de novo sequencing of microbial genomes.

The SoftGenetics NextGENe sequencing software analyses data from multiple applications generated on sequencing platforms and enables the assembly, alignment, quality control and annotation of de novo sequencing. The software’s other applications include: targeted resequencing for single nucleotide polymorphism and insertion/deletion discovery; mate pair analysis; gene expression analysis; chromatin immunoprecipitation (ChIP) sequencing; transcriptome with cDNA analysis; and miRNA discovery and quantification.

Velvet, a short read de novo assembly tool developed by the EBI, is an open-source algorithmic package for assembling short reads into contigs, a continuous sequence of DNA that has been assembled from overlapping cloned DNA fragments. In collaboration with EBI, Applied Biosystems developed a de novo assembly bioinformatics pipeline which can produce scaffolds up to 50 kb and convert colour-space contigs into base-space contigs for easier viewing and analysis. This pipeline provides read-quality filters on colour-space data, conversion into colour-space contigs and final conversion to nucleotide sequences for consensus calling and error correction.