kraken2_read_report: Reads 'kraken2' reports

In larssnip/microclass: Tools for taxonomic classification of prokaryotes

Reads kraken2 reports

Description

Reads the report output from kraken2.

Usage

kraken2_read_report(report.file)

Arguments

report.file

name of file with kraken2 report output.

Details

The report output from kraken2 is a table with one row for each taxon detected by kraken2. Run kraken2 using the --report option to get this convenient summary table.

Note that the software bracken may also output a report in this format.

Value

A data.frame with the kraken2 results for each taxon. It has the columns:

• percent. The percentage of the reads classified to this taxon.

• clade_count. The total number of reads classified to the clade originating from this taxon.

• tax_count. The number of reads assigned directly to this taxon.

• rank. The rank of this taxon in the taxonomy.

• tax_id. The taxonomy identifier of this taxon in the taxonomy.

• name. The name of this taxon in the taxonomy.

Author(s)

Lars Snipen.

See Also

kraken2_read_table, bracken_read_report.

larssnip/microclass documentation built on Nov. 1, 2023, 2:39 p.m.