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A comparison of three programming languages for a full-fledged next-generation sequencing tool.
Pascal Costanza1, Charlotte Herzeel1, Wilfried Verachtert1
1imec, ExaScience Lab, Kapeldreef 75, Leuven, 3001, Belgium.
BMC Bioinformatics
|June 5, 2019
Summary
Go programming language offers the best performance for elPrep, a tool for preparing sequencing data files (SAM/BAM). Benchmarks show Go balances runtime and memory use effectively, outperforming Java and C++17.
Area of Science:
- Bioinformatics
- Computational Biology
- Software Engineering
Background:
- elPrep is a multi-threaded framework for preparing Sequence Alignment Map (SAM) and Binary Alignment Map (BAM) files.
- Heap memory management was a bottleneck in elPrep's original implementation.
- Investigated Go, Java, and C++17 for reimplementing elPrep to address memory management challenges.
Purpose of the Study:
- To evaluate the performance of elPrep reimplemented in Go, Java, and C++17.
- To compare runtime performance and memory usage across the different programming languages.
- To identify the optimal language for elPrep's future development.
Main Methods:
- Reimplemented elPrep in Go, Java, and C++17.
- Benchmarked runtime performance and memory consumption for each implementation.
- Analyzed the effectiveness of concurrent garbage collection (Go, Java) versus reference counting (C++17).
Main Results:
- Go implementation demonstrated the best balance of runtime performance and memory efficiency.
- Java showed slightly faster runtime but significantly higher memory usage compared to Go.
- C++17 implementation was slower and used more memory than Go.
Conclusions:
- Go was selected as the new implementation language for elPrep based on benchmark results.
- Recommends Go as a suitable language for developing other bioinformatics tools for SAM/BAM data processing.
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