Benchmark scripts and programs
Bioinformaticians strive for accurate results, but when time or computational resources are limited, speed can be a factor too. This is especially true when dealing with the huge data sets coming off sequencers these days.
When putting together an analysis pipeline, try taking a small fraction of the data and perform some benchmarking of the available tools.
Benchmarking could be as simple as using time:
time ./script1.sh
time ./script2.sh
But if you need a little more detail, this benchmarking approach captures peak memory usage and average CPU utilisation too.
1. Set up a list of commands/scripts in a file called "codes.txt" Here is a list of commands that I used in a previous post:
$ cat codes.txt
cat test.fastq > /dev/null
zcat test.fastq.gz > /dev/null
bzcat test.fastq.bz2 > /dev/null
pigz -dc test.fastq.gz > /dev/null
pbzip2 -dc test.fastq.bz2 > /dev/null
plzip -dc test.fastq.lz > /dev/null
2. Setup the benchmarking script Use the following script to …
When putting together an analysis pipeline, try taking a small fraction of the data and perform some benchmarking of the available tools.
Benchmarking could be as simple as using time:
time ./script1.sh
time ./script2.sh
But if you need a little more detail, this benchmarking approach captures peak memory usage and average CPU utilisation too.
1. Set up a list of commands/scripts in a file called "codes.txt" Here is a list of commands that I used in a previous post:
$ cat codes.txt
cat test.fastq > /dev/null
zcat test.fastq.gz > /dev/null
bzcat test.fastq.bz2 > /dev/null
pigz -dc test.fastq.gz > /dev/null
pbzip2 -dc test.fastq.bz2 > /dev/null
plzip -dc test.fastq.lz > /dev/null
2. Setup the benchmarking script Use the following script to …