ArticleBioinformatics (Oxford, England)2019
SPRING: a next-generation compressor for FASTQ data.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Dear-OMG: An Omics-General Compression Method for Genomics, Proteomics and Metabolomics Data.Interdisciplinary sciences, computational life sciences · 2026Article
- zDUR: reference-free FASTQ compressor with high compression ratio and speed.BMC bioinformatics · 2026Article
- MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.GigaScience · 2026Article
- FastqCA: an effective FASTQ compressor through 2D spatial redundancy reduction.Frontiers in genetics · 2026Article
- A benchmark study of compression software for human short-read sequence data.Scientific reports · 2025Article
- PgRC2: engineering the compression of sequencing reads.Bioinformatics (Oxford, England) · 2025Article
- Lossless and reference-free compression of FASTQ/A files using GeneSqueeze.Scientific reports · 2025Article
- JARVIS3: an efficient encoder for genomic data.Bioinformatics (Oxford, England) · 2024Article
- Genie: the first open-source ISO/IEC encoder for genomic data.Communications biology · 2024Article
- PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping.Bioinformatics (Oxford, England) · 2024Article
- A compressive seeding algorithm in conjunction with reordering-based compression.Bioinformatics (Oxford, England) · 2024Article
- PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering.BMC bioinformatics · 2023Article
- Reference-free lossless compression of nanopore sequencing reads using an approximate assembly approach.Scientific reports · 2023Article
- Efficient sequencing data compression and FPGA acceleration based on a two-step framework.Frontiers in genetics · 2023Article
- Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.Patterns (New York, N.Y.) · 2022Review
- ACO:lossless quality score compression based on adaptive coding order.BMC bioinformatics · 2022Article
- FCLQC: fast and concurrent lossless quality scores compressor.BMC bioinformatics · 2021Article
- Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression.PLoS computational biology · 2021Article
- The visual story of data storage: From storage properties to user interfaces.Computational and structural biotechnology journal · 2021Review
- Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences.GigaScience · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationHigh-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.
resultsIn 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.