Dynamic Alignment-Free and Reference-Free Read Compression.

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• High throughput sequencing (HTS) generates vast amounts of genomic data, posing significant storage and transmission challenges.
• Pangenomes, collections of highly similar and redundant genomic sequences from large-scale projects, require efficient representation and transfer methods.
• Existing HTS compression tools are not optimized for pangenome data.

Purpose of the Study:

• To introduce a novel compression method, Dynamic Alignment-Free and Reference-Free Read Compression (DARRC), specifically designed for pangenome data.
• To address the limitations of current compression tools in handling the redundancy inherent in large genomic sequence collections.
• To enable efficient storage and transmission of large-scale genomic datasets.

Main Methods:

• Developed DARRC, a new alignment-free and reference-free compression technique.
• Encoded pangenome sequences using a guided de Bruijn graph.
• Implemented incremental updating of DARRC archives without full decompression.

Main Results:

• DARRC effectively compresses both single-end and paired-end read sequences of any length.
• The method utilizes all symbols of the IUPAC nucleotide code.
• On a large Pseudomonas aeruginosa dataset, DARRC achieved a 30% compression ratio improvement over the best state-of-the-art HTS-specific compression method in single-end mode.

Conclusions:

• DARRC presents a significant advancement in pangenome compression, outperforming existing methods.
• The ability to incrementally update archives offers practical advantages for managing growing genomic datasets.
• DARRC provides an efficient solution for the storage and transmission challenges posed by HTS data.