SPRING: A next-generation compressor for FASTQ data

Shubham Chandak, Kedar Tatwawadi, Idoia Ochoa, Mikel Hernaez, Tsachy Weissman

Research output: Contribution to journalArticle

Abstract

Motivation: High-Throughput Sequencing technologies produce huge amounts of data in the form of short genomic reads, associated quality values and read identifiers. Because of the significant structure present in these FASTQ datasets, general-purpose compressors are unable to completely exploit much of the inherent redundancy. Although there has been a lot of work on designing FASTQ compressors, most of them lack in support of one or more crucial properties, such as support for variable length reads, scalability to high coverage datasets, pairing-preserving compression and lossless compression. Results: In this work, we propose SPRING, a reference-free compressor for FASTQ files. SPRING supports a wide variety of compression modes and features, including lossless compression, pairing-preserving compression, lossy compression of quality values, long read compression and random access. SPRING achieves substantially better compression than existing tools, for example, SPRING compresses 195 GB of 25× whole genome human FASTQ from Illumina's NovaSeq sequencer to less than 7 GB, around 1.6× smaller than previous state-of-the-art FASTQ compressors. SPRING achieves this improvement while using comparable computational resources. Availability and implementation: SPRING can be downloaded from https://github.com/shubhamchandak94/SPRING. Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Article numberbty1015
Pages (from-to)2674-2676
Number of pages3
JournalBioinformatics
Volume35
Issue number15
DOIs
StatePublished - Aug 1 2019

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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  • Cite this

    Chandak, S., Tatwawadi, K., Ochoa, I., Hernaez, M., & Weissman, T. (2019). SPRING: A next-generation compressor for FASTQ data. Bioinformatics, 35(15), 2674-2676. [bty1015]. https://doi.org/10.1093/bioinformatics/bty1015