PgRC2: engineering the compression of sequencing reads.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 40037801.
- Also identified by DOI 10.1093/bioinformatics/btaf101 and PMC identifier 11908645.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. PgRC 2.0 can be downloaded from https://github.com/kowallus/PgRC and https://zenodo.org/records/14882486 (10.5281/zenodo.14882486).
Medical subject headings
- High-Throughput Nucleotide Sequencing
- Algorithms
- Data Compression
- Sequence Analysis, DNA
- Software