ngs_backbone, a pipeline for the analisys of new generation sequences

The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is rapidly allowing the discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill this needs we have developed a powerful, yet easy-to-use application. The software ngs_backbone is a parallel pipeline capable of analyzing Sanger, 454, Illumina and Solid sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping, and SNP (single nucleotide polymorphism) calling and selection. In order to build a useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism inside tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina, 23,360 SNVs (single nucleotide variation) were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real.