mineTwister is currently configured run on linux operating systems. This is because of it's dependency on a singularity image of R2DT. Future versions will use the Docker container of R2DT.
To run mineTwister, you need to have several dependencies installed.
- Blast+ command line
wget https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.12.0+-x64-linux.tar.gz
tar -xzvf ncbi-blast-2.12.0+-x64-linux.tar.gz
Next, add the ncbi-blast-2.12.0+-x64-linux/bin folder to your path.
- R2DT
R2DT has its own list of dependencies to run, so, we will use the singularity container instead.
# Download the precompiled data
wget https://ftp.ebi.ac.uk/pub/databases/RNAcentral/r2dt/1.2/cms.tar.gz
tar -xzvf cms.tar.gz
# Build the singularity container
singularity build r2dt docker:https://rnacentral/r2dt
mineTwister can be easily installed with pip using the following command.
pip3 install git+https://github.com/Kobie-Kirven/mineTwister
And that's it! You are ready to start using mineTwister!
In this tutorial, we will walk through a simple example using the Nipponbare IRGSP 1.0 reference genome.
What do you need to run mineTwister?
- all you need is a genome of interest and a concensus twister sequence to search for.
We will download the reference genome using the following command:
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/433/935/GCF_001433935.1_IRGSP-1.0/GCF_001433935.1_IRGSP-1.0_genomic.fna.gz
gunzip GCF_001433935.1_IRGSP-1.0_genomic.fna.gz
Great! Now we have our genome, now all we need is our consensus sequence. We can download this as well:
wget https://github.com/Kobie-Kirven/mineTwister/raw/main/examples/consensus.fa
Cool, now we have everything we need to run mineTwister. Let's make sure that mineTwister is up and running.
minetwister -h
usage: minetwister [-h] -i REFERENCE -c QUERY -s SINGULARITY -d DATA -o OUTPUT
Mine genomes for twister ribozymes
options:
-h, --help show this help message and exit
-i REFERENCE path to reference genome
-c QUERY concensus twister sequence
-s SINGULARITY singularity path
-d DATA singularity data path
-o OUTPUT output
Now let's try to run it for real.
minetwister -i GCF_001433935.1_IRGSP-1.0_genomic.fna -c consensus.fa -s ./r2dt -d ./r2dt-data-cms-dev/ -o rice
You should see a rice.html file and when you open it, it should look like this:
