In this tutorial we will use very small sample genomes to demonstrate how MAGset works. All genome files in this example are in FASTA format. Some results are generated just if the genome files are in GenBank format. After this quick start, please read our tutorial with GenBank files too.
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Descompact the test data
tar -xvzf test-data-quick-start.tar.gz -
At the conf.properties (available inside the test folder), fix the property "genomes_folder", using the absolute path where is the test data genomes_folder and fix the property "output_folder", using absolute path too. If your machine supports less than 8 threads (default value), please change the property threads for the correct number of threads. Example of conf.properties, considering the genomes folder is at /home/fabiosanchez/magset/test/genomes_folder and the output is at /home/fabiosanchez/magset/test/output:
title=MAGset test
genomes_folder=/home/fabiosanchez/magset/test/genomes_folder/
output_folder=/home/fabiosanchez/magset/test/output/
num_threads=8
mag_file=MAG.fasta
reference_genome_files=REF_A.fasta,REF_B.fasta
input_type=FASTA -
Run MAGset script
To run the script, just execute the main script and inform the path of the conf.properties file as first parameter:./run-magset.sh test/conf.properties.
The first run can takes some time, because it is necessary download the docker container. After the script execute, you will see the message "MAGset: done!" at the console. If you receive this message, everything is ok!
Inside the output_folder will be possible see all generated files, including "result" folder, with HTML and CSV results.
The index.html contains the summary of the results:
- ANI matrix;
- Comparison between all genomes using ANI;
- Genomic Region of Interest (GRI) Summary;
- A central concept in MAGset is the Genomic Region of Interest. Please read the MAGset article for more details.
Result screenshot:
