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Data structures and compression algorithms for genomic sequence data.

ABSTRACT: The continuing exponential accumulation of full genome data, including full diploid human genomes, creates new challenges not only for understanding genomic structure, function and evolution, but also for the storage, navigation and privacy of genomic data. Here, we develop data structures and algorithms for the efficient storage of genomic and other sequence data that may also facilitate querying and protecting the data.The general idea is to encode only the differences between a genome sequence and a reference sequence, using absolute or relative coordinates for the location of the differences. These locations and the corresponding differential variants can be encoded into binary strings using various entropy coding methods, from fixed codes such as Golomb and Elias codes, to variables codes, such as Huffman codes. We demonstrate the approach and various tradeoffs using highly variables human mitochondrial genome sequences as a testbed. With only a partial level of optimization, 3615 genome sequences occupying 56 MB in GenBank are compressed down to only 167 KB, achieving a 345-fold compression rate, using the revised Cambridge Reference Sequence as the reference sequence. Using the consensus sequence as the reference sequence, the data can be stored using only 133 KB, corresponding to a 433-fold level of compression, roughly a 23% improvement. Extensions to nuclear genomes and high-throughput sequencing data are discussed.Data are publicly available from GenBank, the HapMap web site, and the MITOMAP database. Supplementary materials with additional results, statistics, and software implementations are available from http://mammag.web.uci.edu/bin/view/Mitowiki/ProjectDNACompression.

SUBMITTER: Brandon MC

PROVIDER: S-EPMC2705231 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

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Data structures and compression algorithms for genomic sequence data.

Brandon Marty C MC Wallace Douglas C DC Baldi Pierre P

Bioinformatics (Oxford, England) 20090515 14

<h4>Motivation</h4>The continuing exponential accumulation of full genome data, including full diploid human genomes, creates new challenges not only for understanding genomic structure, function and evolution, but also for the storage, navigation and privacy of genomic data. Here, we develop data structures and algorithms for the efficient storage of genomic and other sequence data that may also facilitate querying and protecting the data.<h4>Results</h4>The general idea is to encode only the d ...[more]

PMID: 19447783

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Project description:MotivationThe high throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for the computational infrastructure. Data management, storage and analysis have become major logistical obstacles for those adopting the new platforms. The requirement for large investment for this purpose almost signalled the end of the Sequence Read Archive hosted at the National Center for Biotechnology Information (NCBI), which holds most of the sequence data generated world wide. Currently, most HTS data are compressed through general purpose algorithms such as gzip. These algorithms are not designed for compressing data generated by the HTS platforms; for example, they do not take advantage of the specific nature of genomic sequence data, that is, limited alphabet size and high similarity among reads. Fast and efficient compression algorithms designed specifically for HTS data should be able to address some of the issues in data management, storage and communication. Such algorithms would also help with analysis provided they offer additional capabilities such as random access to any read and indexing for efficient sequence similarity search. Here we present SCALCE, a 'boosting' scheme based on Locally Consistent Parsing technique, which reorganizes the reads in a way that results in a higher compression speed and compression rate, independent of the compression algorithm in use and without using a reference genome.ResultsOur tests indicate that SCALCE can improve the compression rate achieved through gzip by a factor of 4.19-when the goal is to compress the reads alone. In fact, on SCALCE reordered reads, gzip running time can improve by a factor of 15.06 on a standard PC with a single core and 6 GB memory. Interestingly even the running time of SCALCE + gzip improves that of gzip alone by a factor of 2.09. When compared with the recently published BEETL, which aims to sort the (inverted) reads in lexicographic order for improving bzip2, SCALCE + gzip provides up to 2.01 times better compression while improving the running time by a factor of 5.17. SCALCE also provides the option to compress the quality scores as well as the read names, in addition to the reads themselves. This is achieved by compressing the quality scores through order-3 Arithmetic Coding (AC) and the read names through gzip through the reordering SCALCE provides on the reads. This way, in comparison with gzip compression of the unordered FASTQ files (including reads, read names and quality scores), SCALCE (together with gzip and arithmetic encoding) can provide up to 3.34 improvement in the compression rate and 1.26 improvement in running time.AvailabilityOur algorithm, SCALCE (Sequence Compression Algorithm using Locally Consistent Encoding), is implemented in C++ with both gzip and bzip2 compression options. It also supports multithreading when gzip option is selected, and the pigz binary is available. It is available at http://scalce.sourceforge.net.Contactfhach@cs.sfu.ca or cenk@cs.sfu.caSupplementary informationSupplementary data are available at Bioinformatics online.

Project description:BACKGROUND:Recent advancements in high-throughput sequencing technologies have generated an unprecedented amount of genomic data that must be stored, processed, and transmitted over the network for sharing. Lossy genomic data compression, especially of the base quality values of sequencing data, is emerging as an efficient way to handle this challenge due to its superior compression performance compared to lossless compression methods. Many lossy compression algorithms have been developed for and evaluated using DNA sequencing data. However, whether these algorithms can be used on RNA sequencing (RNA-seq) data remains unclear. RESULTS:In this study, we evaluated the impacts of lossy quality value compression on common RNA-seq data analysis pipelines including expression quantification, transcriptome assembly, and short variants detection using RNA-seq data from different species and sequencing platforms. Our study shows that lossy quality value compression could effectively improve RNA-seq data compression. In some cases, lossy algorithms achieved up to 1.2-3 times further reduction on the overall RNA-seq data size compared to existing lossless algorithms. However, lossy quality value compression could affect the results of some RNA-seq data processing pipelines, and hence its impacts to RNA-seq studies cannot be ignored in some cases. Pipelines using HISAT2 for alignment were most significantly affected by lossy quality value compression, while the effects of lossy compression on pipelines that do not depend on quality values, e.g., STAR-based expression quantification and transcriptome assembly pipelines, were not observed. Moreover, regardless of using either STAR or HISAT2 as the aligner, variant detection results were affected by lossy quality value compression, albeit to a lesser extent when STAR-based pipeline was used. Our results also show that the impacts of lossy quality value compression depend on the compression algorithms being used and the compression levels if the algorithm supports setting of multiple compression levels. CONCLUSIONS:Lossy quality value compression can be incorporated into existing RNA-seq analysis pipelines to alleviate the data storage and transmission burdens. However, care should be taken on the selection of compression tools and levels based on the requirements of the downstream analysis pipelines to avoid introducing undesirable adverse effects on the analysis results.

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Data structures and compression algorithms for genomic sequence data.

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Data structures and compression algorithms for genomic sequence data.

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