PgRC2: engineering the compression of sequencing reads.

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

SUBMITTER: Kowalski TM 

PROVIDER: S-EPMC11908645 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature