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CMIC: an efficient quality score compressor with random access functionality
BACKGROUND: Over the past few decades, the emergence and maturation of new technologies have substantially reduced the cost of genome sequencing. As a result, the amount of genomic data that needs to be stored and transmitted has grown exponentially. For the standard sequencing data format, FASTQ, c...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9308261/ https://www.ncbi.nlm.nih.gov/pubmed/35870880 http://dx.doi.org/10.1186/s12859-022-04837-1 |
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author | Chen, Hansen Chen, Jianhua Lu, Zhiwen Wang, Rongshu |
author_facet | Chen, Hansen Chen, Jianhua Lu, Zhiwen Wang, Rongshu |
author_sort | Chen, Hansen |
collection | PubMed |
description | BACKGROUND: Over the past few decades, the emergence and maturation of new technologies have substantially reduced the cost of genome sequencing. As a result, the amount of genomic data that needs to be stored and transmitted has grown exponentially. For the standard sequencing data format, FASTQ, compression of the quality score is a key and difficult aspect of FASTQ file compression. Throughout the literature, we found that the majority of the current quality score compression methods do not support random access. Based on the above consideration, it is reasonable to investigate a lossless quality score compressor with a high compression rate, a fast compression and decompression speed, and support for random access. RESULTS: In this paper, we propose CMIC, an adaptive and random access supported compressor for lossless compression of quality score sequences. CMIC is an acronym of the four steps (classification, mapping, indexing and compression) in the paper. Its framework consists of the following four parts: classification, mapping, indexing, and compression. The experimental results show that our compressor has good performance in terms of compression rates on all the tested datasets. The file sizes are reduced by up to 21.91% when compared with LCQS. In terms of compression speed, CMIC is better than all other compressors on most of the tested cases. In terms of random access speed, the CMIC is faster than the LCQS, which provides a random access function for compressed quality scores. CONCLUSIONS: CMIC is a compressor that is especially designed for quality score sequences, which has good performance in terms of compression rate, compression speed, decompression speed, and random access speed. The CMIC can be obtained in the following way: https://github.com/Humonex/Cmic. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04837-1. |
format | Online Article Text |
id | pubmed-9308261 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-93082612022-07-24 CMIC: an efficient quality score compressor with random access functionality Chen, Hansen Chen, Jianhua Lu, Zhiwen Wang, Rongshu BMC Bioinformatics Software BACKGROUND: Over the past few decades, the emergence and maturation of new technologies have substantially reduced the cost of genome sequencing. As a result, the amount of genomic data that needs to be stored and transmitted has grown exponentially. For the standard sequencing data format, FASTQ, compression of the quality score is a key and difficult aspect of FASTQ file compression. Throughout the literature, we found that the majority of the current quality score compression methods do not support random access. Based on the above consideration, it is reasonable to investigate a lossless quality score compressor with a high compression rate, a fast compression and decompression speed, and support for random access. RESULTS: In this paper, we propose CMIC, an adaptive and random access supported compressor for lossless compression of quality score sequences. CMIC is an acronym of the four steps (classification, mapping, indexing and compression) in the paper. Its framework consists of the following four parts: classification, mapping, indexing, and compression. The experimental results show that our compressor has good performance in terms of compression rates on all the tested datasets. The file sizes are reduced by up to 21.91% when compared with LCQS. In terms of compression speed, CMIC is better than all other compressors on most of the tested cases. In terms of random access speed, the CMIC is faster than the LCQS, which provides a random access function for compressed quality scores. CONCLUSIONS: CMIC is a compressor that is especially designed for quality score sequences, which has good performance in terms of compression rate, compression speed, decompression speed, and random access speed. The CMIC can be obtained in the following way: https://github.com/Humonex/Cmic. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04837-1. BioMed Central 2022-07-23 /pmc/articles/PMC9308261/ /pubmed/35870880 http://dx.doi.org/10.1186/s12859-022-04837-1 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Chen, Hansen Chen, Jianhua Lu, Zhiwen Wang, Rongshu CMIC: an efficient quality score compressor with random access functionality |
title | CMIC: an efficient quality score compressor with random access functionality |
title_full | CMIC: an efficient quality score compressor with random access functionality |
title_fullStr | CMIC: an efficient quality score compressor with random access functionality |
title_full_unstemmed | CMIC: an efficient quality score compressor with random access functionality |
title_short | CMIC: an efficient quality score compressor with random access functionality |
title_sort | cmic: an efficient quality score compressor with random access functionality |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9308261/ https://www.ncbi.nlm.nih.gov/pubmed/35870880 http://dx.doi.org/10.1186/s12859-022-04837-1 |
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