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Bioinformatics. 2012 Mar 1;28(5):628-35. doi: 10.1093/bioinformatics/btr689. Epub 2011 Dec 13.

Transformations for the compression of FASTQ quality scores of next-generation sequencing data.

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  • 1Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Chiba-ken 277-8561, Tokyo 135-0064, Japan.



The growth of next-generation sequencing means that more effective and efficient archiving methods are needed to store the generated data for public dissemination and in anticipation of more mature analytical methods later. This article examines methods for compressing the quality score component of the data to partly address this problem.


We compare several compression policies for quality scores, in terms of both compression effectiveness and overall efficiency. The policies employ lossy and lossless transformations with one of several coding schemes. Experiments show that both lossy and lossless transformations are useful, and that simple coding methods, which consume less computing resources, are highly competitive, especially when random access to reads is needed.


Our C++ implementation, released under the Lesser General Public License, is available for download at


Supplementary data are available at Bioinformatics online.

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