Related Experiment Video
Updated: May 24, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
PgRC2: engineering the compression of sequencing reads
Tomasz M Kowalski1, Szymon Grabowski1
1Institute 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. 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).
Related Concept Videos
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Next-generation Sequencing
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Sanger Sequencing
Maxam-Gilbert Sequencing
Challenges of the Maxam-Gilbert Method
The...

