classify taxonomy

virpipe classify-taxonomy --image IMAGE --prefix PREFIX \
                                 [--outdir OUTDIR] [--resume] \
                                 --platform [{illumina,nanopore}] \
                                 --fastq FASTQ [--fastq2 FASTQ2] \
                                 [--kraken2-confidence-threshold 0.1] \
                                 [--kraken2-db [KRAKEN2_DB]] \
                                 [--centrifuge-db [CENTRIFUGE_DB]]

The task classify-taxonomy is for classifying each read into a taxonomy using the k-mer matching strategy. Kraken2 and Centrifuge are used for illumina and nanopore reads, respectively. And the classification results are visualized as heatmaps and krona charts.

Used tools

• Nanopore: Centrifuge
• Illumina: Kraken2
• Krona, MetaComp

Options

• --kraken2-confidence-threshold: (Float, default 0.1) In Kraken2, each classification of a read is assigned a confidence score. The classifications with scores less than the threshold will be regarded as unclassified.
• --kraken2-db: (Directory) Database for Kraken2. It should be the path of a directory containing files such as .k2d and so on.
• --centrifuge-db: (Path) Database for Centrifuge. Please note that it should be the directory + basename of indexes. For example, if the path of the database directory is /path/to/dir/centrifuge_db and it contains indexes such as abv.1.cf, abv.2.cf, and so on, /path/to/dir/centrifuge_db/abv should be given to this option.