Performance comparison of Go, C++ and Java for biological sequencing tool

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PDF: https://www.biorxiv.org/content/biorxiv/early/2019/02/22/558056.full.pdf

PDF Mirror: https://mega.nz/#!ft8xECJb!PokLtot2rUDSbz2rPOhfwbMAhfLaTsbvrcF5cF640M0

Paper: https://www.biorxiv.org/content/10.1101/558056v1

Conclusion:

Due to the concurrency and parallelism of Go’s and Java’s garbage collectors, the elPrep reimplementations in these programming languages perform significantly faster than the C++17 implementations which relies on reference counting. Since the Go implementation uses significantly less heap memory than the Java implementation, we therefore decided to base the official elPrep implementation since version 3.0 on Go. Based on our positive experiences, we recommend authors of other bionformatics tools for processing SAM/BAM data, and potentially also other sequencing data formats, to also consider Go as an implementation language.

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