LFastqC: A lossless non-reference-based FASTQ compressor.
The cost-effectiveness of next-generation sequencing (NGS) has led to the advancement of genomic research, thereby regularly generating a large amount of raw data that often requires efficient infrastructures such as data centers to manage the storage and transmission of such data. The generated NGS...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2019-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0224806 |
| _version_ | 1818677949077913600 |
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| author | Sultan Al Yami Chun-Hsi Huang |
| author_facet | Sultan Al Yami Chun-Hsi Huang |
| author_sort | Sultan Al Yami |
| collection | DOAJ |
| description | The cost-effectiveness of next-generation sequencing (NGS) has led to the advancement of genomic research, thereby regularly generating a large amount of raw data that often requires efficient infrastructures such as data centers to manage the storage and transmission of such data. The generated NGS data are highly redundant and need to be efficiently compressed to reduce the cost of storage space and transmission bandwidth. We present a lossless, non-reference-based FASTQ compression algorithm, known as LFastqC, an improvement over the LFQC tool, to address these issues. LFastqC is compared with several state-of-the-art compressors, and the results indicate that LFastqC achieves better compression ratios for important datasets such as the LS454, PacBio, and MinION. Moreover, LFastqC has a better compression and decompression speed than LFQC, which was previously the top-performing compression algorithm for the LS454 dataset. LFastqC is freely available at https://github.uconn.edu/sya12005/LFastqC. |
| first_indexed | 2024-12-17T09:07:29Z |
| format | Article |
| id | doaj.art-a16cd1f2cd7c46079328194375dbb754 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-17T09:07:29Z |
| publishDate | 2019-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-a16cd1f2cd7c46079328194375dbb7542022-12-21T21:55:24ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-011411e022480610.1371/journal.pone.0224806LFastqC: A lossless non-reference-based FASTQ compressor.Sultan Al YamiChun-Hsi HuangThe cost-effectiveness of next-generation sequencing (NGS) has led to the advancement of genomic research, thereby regularly generating a large amount of raw data that often requires efficient infrastructures such as data centers to manage the storage and transmission of such data. The generated NGS data are highly redundant and need to be efficiently compressed to reduce the cost of storage space and transmission bandwidth. We present a lossless, non-reference-based FASTQ compression algorithm, known as LFastqC, an improvement over the LFQC tool, to address these issues. LFastqC is compared with several state-of-the-art compressors, and the results indicate that LFastqC achieves better compression ratios for important datasets such as the LS454, PacBio, and MinION. Moreover, LFastqC has a better compression and decompression speed than LFQC, which was previously the top-performing compression algorithm for the LS454 dataset. LFastqC is freely available at https://github.uconn.edu/sya12005/LFastqC.https://doi.org/10.1371/journal.pone.0224806 |
| spellingShingle | Sultan Al Yami Chun-Hsi Huang LFastqC: A lossless non-reference-based FASTQ compressor. PLoS ONE |
| title | LFastqC: A lossless non-reference-based FASTQ compressor. |
| title_full | LFastqC: A lossless non-reference-based FASTQ compressor. |
| title_fullStr | LFastqC: A lossless non-reference-based FASTQ compressor. |
| title_full_unstemmed | LFastqC: A lossless non-reference-based FASTQ compressor. |
| title_short | LFastqC: A lossless non-reference-based FASTQ compressor. |
| title_sort | lfastqc a lossless non reference based fastq compressor |
| url | https://doi.org/10.1371/journal.pone.0224806 |
| work_keys_str_mv | AT sultanalyami lfastqcalosslessnonreferencebasedfastqcompressor AT chunhsihuang lfastqcalosslessnonreferencebasedfastqcompressor |