An experimental sorting method for improving metagenomic data encoding
Fuente:
arXiv
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Preprint |
| Published: |
2024
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866913184633323520 |
|---|---|
| author | Pratas, Diogo Pinho, Armando J. |
| author_facet | Pratas, Diogo Pinho, Armando J. |
| contents | Minimizing data storage poses a significant challenge in large-scale metagenomic projects. In this paper, we present a new method for improving the encoding of FASTQ files generated by metagenomic sequencing. This method incorporates metagenomic classification followed by a recursive filter for clustering reads by DNA sequence similarity to improve the overall reference-free compression. In the results, we show an overall improvement in the compression of several datasets. As hypothesized, we show a progressive compression gain for higher coverage depth and number of identified species. Additionally, we provide an implementation that is freely available at https://github.com/cobilab/mizar and can be customized to work with other FASTQ compression tools. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2401_01786 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | An experimental sorting method for improving metagenomic data encoding Pratas, Diogo Pinho, Armando J. Information Theory Genomics Minimizing data storage poses a significant challenge in large-scale metagenomic projects. In this paper, we present a new method for improving the encoding of FASTQ files generated by metagenomic sequencing. This method incorporates metagenomic classification followed by a recursive filter for clustering reads by DNA sequence similarity to improve the overall reference-free compression. In the results, we show an overall improvement in the compression of several datasets. As hypothesized, we show a progressive compression gain for higher coverage depth and number of identified species. Additionally, we provide an implementation that is freely available at https://github.com/cobilab/mizar and can be customized to work with other FASTQ compression tools. |
| title | An experimental sorting method for improving metagenomic data encoding |
| topic | Information Theory Genomics |
| url | https://arxiv.org/abs/2401.01786 |