{"title":"PgRC2: engineering the compression of sequencing reads.","authors":"Tomasz M Kowalski, Szymon Grabowski","doi":"10.1093/bioinformatics/btaf101","DOIUrl":null,"url":null,"abstract":"<p><strong>Summary: </strong>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.</p><p><strong>Availability and implementation: </strong>PgRC 2.0 can be downloaded from https://github.com/kowallus/PgRC and https://zenodo.org/records/14882486 (10.5281/zenodo.14882486).</p>","PeriodicalId":93899,"journal":{"name":"Bioinformatics (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":5.4000,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908645/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics (Oxford, England)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioinformatics/btaf101","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
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).
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