This is a tool that benchmarks performance and CPU footprint bioinformatics and genomic analysis tools particularly MSA, phyllo tools using our base debigenic genomic and bioinformatic analysis pipeline.
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BEDTools
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Clustalw2
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BLAST
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HMMER
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PHYLIP
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TODO: QuEST
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TODO: VELVET
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TODO: MUMMER
We benchmarked performance of 5+ bioinformatic tools for MSA, Philo etc run on a debian linux machine pipeline.
This benchmark setup currently works with my debigenic genomic and bioinformatics pipeline that runs on Ubuntu 22.04 , you can pull the docker image and clone this repo on the pipeline before you continue
docker pull propenster/debigenic
docker run -it propenster/debigenic bin/bash
git clone https://github.com/propenster/biobencher.git
cd ./biobencher
./BioBencher
N.B: You may need to make the app an executable first, you may do so by running the below command on linux
chmod +x ./BioBencher