Ngs backbone

Ngs backbone performs analysis of Sanger, 454, Illumina, and SOLiD sequencing data to enable read cleaning, mapping, de novo transcriptome assembly, annotation, and SNP/SNV discovery for genetic research.

Key Features:

• Parallel Pipeline Architecture: Engineered as a parallel pipeline enabling efficient processing of large datasets across Sanger, 454, Illumina, and SOLiD sequencing technologies.
• Read Cleaning: Performs read cleaning to produce high-quality input for downstream analyses.
• Transcriptome Assembly and Annotation: Supports de novo transcriptome assembly and annotation of transcriptomic data.
• Read Mapping: Maps sequence reads against reference genomes or transcriptomes for downstream variant and expression analyses.
• SNP Calling and Selection: Calls and selects single nucleotide polymorphisms (SNPs) and single nucleotide variations (SNVs) for genetic studies and marker development.

Scientific Applications:

• SNP/SNV Discovery in Non-model Species: Enables rapid discovery and selection of SNPs/SNVs from combined NGS and Sanger datasets for non-model organisms.
• Integration with High-throughput Genotyping: Produces polymorphism candidates suitable for downstream high-throughput genotyping workflows.
• Genetic Research and Crop Improvement: Facilitates generation of polymorphic SNV collections to support genetic studies and breeding programs.

Methodology:

Public tomato Sanger EST reads were combined with 14.2 million Illumina reads, reads were cleaned and mapped to the Solanum lycopersicum Genomics Network (SGN) tomato transcriptome (coverage 4.2 for Sanger, 8.5 for Illumina), predicting 23,360 SNVs of which 76 were experimentally validated with 85% accuracy.