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Vertical lossless genomic data compression tools for assembled genomes: A systematic literature review
Kelvin V Kredens1, Juliano V Martins1, Osmar B Dordal2
1Graduate Program in Informatics (PPGia), Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil.
Plos One
|May 27, 2020
Summary
Genomic data compression is essential due to decreasing sequencing costs. Vertical compression tools leverage sequence similarity, but a standardized evaluation protocol is missing for comparing their execution flows.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Decreasing costs and time for genome sequencing and assembly have increased demand for biological data storage.
- Vertical compression tools utilize high similarity between genomic sequences for efficient data compression.
Purpose of the Study:
- To systematically review and compare existing vertical compression tools for assembled genomic sequences.
- To analyze the execution flow, including preprocessing, transformation, and data encoding phases, of these tools.
Main Methods:
- Systematic literature review conducted on PubMed and Scopus databases.
- Selection of 32 relevant papers from 45,726 initial papers based on specific inclusion criteria.
- Focus on lossless vertical compression tools manipulating FASTA format genomic sequences without prior knowledge.
Main Results:
- Identified various vertical compression tools for assembled genomic sequences.
- Extracted performance compression results, but direct comparison was not feasible.
- Observed a lack of standardized evaluation protocols across the reviewed tools.
Conclusions:
- A critical need exists for a standardized evaluation protocol for vertical compression tools.
- Standardization is necessary for reliable comparison of tool performance and execution flows.
- Further research should focus on developing and implementing such protocols to advance genomic data compression.
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