Clean reads

Clean reads processes next-generation sequencing (NGS) data from Sanger, 454, Illumina, and SOLiD platforms to trim adaptors and low-quality regions and produce cleaned reads for downstream analyses such as transcriptome assembly, read mapping, and SNP discovery.

Key Features:

• Read cleaning: Trims low-quality regions and removes adaptors, vectors, and unwanted sequences defined by regular expressions.
• Quality filtering: Removes reads that do not meet predefined quality criteria.
• Parallel processing pipeline (ngs_backbone): Executes cleaning and downstream steps within a parallel pipeline framework to scale to large NGS datasets.
• Platform support: Accepts input from Sanger EST reads, 454, Illumina, and SOLiD sequencing technologies.
• Transcriptome assembly and annotation support: Prepares cleaned reads for construction and functional annotation of transcriptomes.
• Read mapping: Aligns cleaned reads to reference genomes or transcriptomes, including mapping to the SGN tomato transcriptome.
• SNP calling and selection: Identifies single nucleotide polymorphisms and reports predicted single nucleotide variations (SNVs).

Scientific Applications:

• SNP discovery in non-model species: Enables identification and selection of SNPs from diverse organisms by processing data from multiple sequencing platforms.
• Tomato (Solanum lycopersicum) case study: Processed Sanger EST reads and Illumina data, mapped to the SGN tomato transcriptome, predicting 23,360 SNVs with 85% experimental validation.

Methodology:

Trimming of low-quality regions, adaptor and vector removal using regular expressions, quality-based read filtering, parallel execution within the ngs_backbone pipeline, read mapping to reference genomes/transcriptomes, and SNP calling; integration with high-throughput genotyping data and NGS data analysis.