Create a Subtraction Updated February 5, 2020

Subtractions are whole genome references used for eliminating reads from the analysis that are likely to have originated from the host genome or non-pathogenic organisms associated with the host such as insects or fungi.

Find source FASTA

We will use the Arabidopsis thaliana genome for this example.

Go to the Ensembl Genomes FTP site for Arabidopsis here. Download the unmasked version of the genome.

“Download Arabidopsis Genome”

Decompress the downloaded file. Virtool does not currently accept GZIP-compressed subtraction FASTA data.

Upload FASTA

Go to the Subtraction view via the main navigation bar. You should see the following:

“Main Subtraction View”

Click on the Files link in the left sidebar to go to the subtraction file manager.

“Subtraction File Manager

Upload the previously obtained FASTA file.

Create Subtraction

Go to the Subtraction view via the main navigation bar.

Subtraction Listing

Click the button to open the subtraction creation dialog.

Creation Dialog

Enter a unique name and an optional nickname, select the FASTA file, and click Start to start the job.

Filled Creation Dialog

While the subtraction is being created it will have an Importing label.

Subtraction Importing

Wait for the job to complete before trying to use the new subtraction. You can view its progress by going to the Jobs view.

Subtraction Job in Progress

The subtraction will have the Ready label when it is ready to use.

Subtraction Ready

View detailed information for the subtraction by clicking on it. As you use the subtraction in samples, they will be added to the Linked Samples list.

Subtraction Detail