Biofast is a small benchmark for evaluating the performance of programming languages and implementations on a few common tasks in the field of Bioinformatics. It currently includes two benchmarks: FASTQ parsing and interval query. Please see also the companion blog post.
Setup
We ran the test on a CentOS 7 server with two EPYC 7301 CPUs and 1TB memory. The system comes with gcc-4.8.5, python-3.7.6, nim-1.2.0, julia-1.4.1, go-1.14.3, luajit-322db02 and k8-0.2.5. Relatively small libraries are included in the lib directory directory.
We tried to avoid other active processes when test programs were running. Timing in this page was obtained with hyperfine, which reports CPU time averaged in at least ten rounds. Peak memory was often measured only once as hyperfine doesn't report memory usage.
Full results can be found in the fqcnt and bedcov directories, respectively. This README only shows one implementation per language. We exclude those binding to C libraries and try to select the one implementing a similar algorithm to the C version.
github地址：https://github.com/lh3/biofast