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).
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908645 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btaf101 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
PgRC2: engineering the compression of sequencing reads.
Bioinformatics
March 2025
Institute of Applied Computer Science, Lodz University of Technology, Lodz 90-924, Poland.
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.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!