Work

PgRC2: engineering the compression of sequencing reads

Year: 2025

Type: article

Abstract: SUMMARY: The FASTQ format remains at the heart of high-throughput sequencing. Despite advances in specialized FASTQ compressors, they are still imperfect in terms of practical performance tradeoffs. We present a multi-threaded version of Pseudogenome-based Read Compressor (PgRC), an in-memory algorithm for compressing the DNA stream, based on the idea of approximating the shortest common superstring over high-quality reads. Redundancy in the obtained string is efficiently removed by using a compact temporary representation. The current version, v2.0, preserves the compression ratio of the previous one, reducing the compression (resp. decompression) time by a factor of 8-9 (resp. 2-2.5) on a 14-core/28-thread machine. AVAILABILITY AND IMPLEMENTATION: PgRC 2.0 can be downloaded from https://github.com/kowallus/PgRC and https://zenodo.org/records/14882486 (10.5281/zenodo.14882486).

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btaf101

Authors: Tomasz M Kowalski, Szymon Grabowski

Institution: Lodz University of Technology

Language: English

Topic: Algorithms and Data Compression

Subfield: Artificial Intelligence

Field: Computer Science

Domain: Physical Sciences

Open Access status: gold

Estimated APC paid: $3,989

Funder: Politechnika Lódzka