/biobencher

This is a benchmark of bioinformatics and genomic analysis tools particularly MSA, phyllo tools using our base debigenic genomic and bioinformatic analysis pipeline

Primary LanguageC#

biobencher

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.

Tools Benchmarked

  • BEDTools

  • Clustalw2

  • BLAST

  • HMMER

  • PHYLIP

  • TODO: QuEST

  • TODO: VELVET

  • 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

How to Run

Step 1 - pull debigenic pipeline image from dockerhub

docker pull propenster/debigenic

Step 2 - Run the pipeline image

docker run -it propenster/debigenic bin/bash

clone this repo

git clone https://github.com/propenster/biobencher.git

cd into ./biobencher

cd ./biobencher

Run the Tool ./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