--db, the output with
--output, the report with
--reportand the read files. We also need to tell kraken2 that the files are paired. For readers who are using the s3 server the databases are located at /opt/storage2/db/kraken2/. We will be using the standard database, which contains sequences from viruses, bacteria and human.
lesson the terminal or any other text editor/viewer. The format of the report is the following:
extract_classified_reads.pyscript which we installed earlier. We can either tell the script to extract or exclude reads from a tax-tree. We will also need to pass a file to the script which contains the taxonomic IDs from the NCBI. If you are reading this and have access to the s3 node then it is located at /opt/storage2/db/kraken2/nodes.dmp.
ERR2513180_2.kraken2_filt.fastq.gzwhich contain the filtered reads.