Test your installation

After you installed reper, you can test the functionality using the provided testdata:

preparation

• cd to the reper directory
• cd to the test/ subdirectory
• extract the testdata: tar xzf testdata.tar.gz

The two fastq files used here are randomly sampled subsets from the Beta vulgaris dataset used in the tutorial.

test database configuration

• run reper configure-refseq and reper configure-REdat
• Now you should have a databases/ directory with two subdirectories and sequences with blast-db files

test the reper pipeline

• Note: Since Trinity requires a lot of resources, the default limits are 2 CPU threads and 12G memory
• start reper: reper kmerCount.
• At the end, you should get three landscape files (repeat-landscape_by-*).
• Check reper.log for errors, if you did not get the three result files