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Example

This example demonstrates how to classify RNA-seq reads from a COVID-19 patient using the RefSeq Virus database. The whole process takes less than 10 minutes on a personal machine.

Step 1 — Download the RefSeq Virus Database (8.1 GiB)

Link: https://steineggerlab.s3.amazonaws.com/metabuli/archive/refseq_virus.tar.gz

Step 2 — Download RNA-seq reads (SRR14484345)

fasterq-dump --split-files SRR14484345

Tip

Download SRA Toolkit containing fasterq-dump from https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit.

Step 3 — Classify reads

metabuli classify \
    SRR14484345_1.fq SRR14484345_2.fq \
    OUTDIR/refseq_virus \
    RESULT_DIR JOB_ID \
    --max-ram RAM_SIZE

Replace RAM_SIZE with the amount of RAM (in GiB) available on your machine.

Step 4 — Inspect the report

Open RESULT_DIR/JOB_ID_report.tsv and look for a section like the following:

92.2331  510490  442     species  694009   Severe acute respiratory syndrome-related coronavirus
92.1433  509993  509993  no rank  2697049  Severe acute respiratory syndrome coronavirus 2

This shows that ~92% of reads were classified to SARS-CoV-2.

Next Steps

  • Use refine-results to filter or adjust the classification results.
  • Use extract to pull out reads classified to a specific taxon.
  • Browse the interactive taxonomy chart in RESULT_DIR/JOB_ID_krona.html.