AUSPP

AUSPP performs preprocessing and mapping of next-generation sequencing (NGS) short reads to prepare raw sequencing data for downstream genomic analysis.

Key Features:

• Read Quality Control: Filters raw sequencing reads to retain high-quality data for downstream processing.
• Adaptor Trimming: Removes sequencing adapter sequences and other unwanted fragments from raw reads.
• Read Collapsing: Collapses identical reads to reduce redundancy and computational load during mapping.
• Structural RNA Filtering: Identifies and removes structural RNA sequences that may interfere with analysis of other genomic elements.
• Length Selection: Allows selection of reads based on specified sequence length criteria.
• Reference Mapping: Maps processed reads to reference genomes or sequences using short-read aligners that accept FASTQ input.
• Normalized Wiggle File Generation: Produces normalized wiggle files for visualization and analysis of genomic read coverage.

Scientific Applications:

• NGS Data Preprocessing: Standardizes preprocessing of short-read sequencing datasets prior to alignment and downstream analysis.
• Comparative Genomic Meta-Analysis: Enables consistent processing of sequencing datasets from multiple studies for integrative analyses.
• Genome Coverage Analysis: Supports visualization and analysis of sequencing read coverage across genomic regions.

Methodology:

AUSPP processes raw NGS reads through quality control, adaptor trimming, read collapsing, structural RNA removal, and length filtering, followed by mapping to reference genomes and generation of normalized wiggle coverage files.