ALFA: annotation landscape for aligned reads.

Area of Science:

• Genomics
• Bioinformatics

Background:

• Next-Generation Sequencing (NGS) has revolutionized functional genomics.
• Standard NGS analysis involves read quality control and genome mapping.
• Post-mapping quality control tools are limited in scope and applicability.

Purpose of the Study:

• To introduce ALFA, a universal tool for post-mapping quality control in NGS data analysis.
• To provide a simple, broadly applicable framework for analyzing aligned NGS reads.
• To facilitate a global overview of NGS data using genomic annotations.

Main Methods:

• ALFA processes aligned NGS datasets for any organism with available genomic annotations.
• The tool computes and displays read distribution by genomic categories (exon, intron, UTR) and biotypes (protein-coding, miRNA).
• ALFA operates via a single command-line interface with nucleotide precision.

Main Results:

• ALFA demonstrates versatility across diverse NGS applications including Ribo-Seq, RNA-Seq, CLIP-Seq, Bisulfite sequencing, and ChIP-Seq.
• Applications were shown on multiple model organisms: Homo sapiens, Mus musculus, Saccharomyces cerevisiae, Arabidopsis thaliana, and Caenorhabditis elegans.
• The tool provides detailed read distribution analysis for quality assessment.

Conclusions:

• ALFA offers a powerful and widely applicable solution for post-mapping quality control in NGS.
• It generates a global overview of NGS data, enhancing interpretation through common or dedicated annotations.
• ALFA is accessible as an easy-to-install command-line tool and via the Galaxy Tool Shed.