Importing a pre-built kraken2 reference library

kraken2 is used by three processes within the Core Tool: kraken2, kraken2_miniKraken and kraken2_QC.

Prebuilt kraken2 reference libraries can be found on Ben Langmead's Github page. Ben Langmead is one of the contributers to kraken2.

  1. Navigate to the scripts folder by entering cd /genomics/home/vol-genomics/genome_tools/reference_libraries.
  2. Enter curl -o file_name address , substituting file_name and address, and wait for the file to transfer completely.
  3. Unpack using tar -zxvf file_name.tar.gz, substituting file_name.

To use server space efficiently, the file_name.tar.gz can now be delete, and any older version.

CURL example

To copy URL, or curl, the stardard kraken2 database originally generated on 17th May 2021 and limited to 8 Gb use:

curl -o k2_standard_8gb_20210517.tar.gz https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz

Tips

Keep the original file name to remind you origin of the library.

Find the URL by right-clicking over the item you want to transfer in the HTTPS URL column on Ben Langmead's website, and selecting Copy Link.