bracken_read_report: Reads bracken reports

In larssnip/microclass: Tools for taxonomic classification of prokaryotes

Reads bracken reports

Description

Reads the report output from bracken.

Usage

bracken_read_report(report.file)

Arguments

report.file

name of file with bracken report output.

Details

The report output from bracken is a table with one row for each taxon with assigned reads. This is the file produced by bracken using the -o option.

Note that by the -w option bracken will output a report in kraken2 format, see kraken2_read_report.

Value

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

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

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

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

• tax_count_krk. The number of reads classified to this taxon by kraken2.

• added_brk. The additional reads assigned by bracken.

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

• fraction. The fraction of the total number of reads assigned to this taxon.

Author(s)

Lars Snipen.

See Also

kraken2_read_report.

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