kraken2_read_table: Reads raw 'kraken2' output

In larssnip/microclass: Tools for taxonomic classification of prokaryotes

Reads raw kraken2 output

Description

Reads the raw output table from kraken2.

Usage

kraken2_read_table(krk.file, filter = TRUE)

Arguments

krk.file	name of file with raw kraken2 output.
filter.	returns only classified reads if TRUE.

Details

The raw output from kraken2 is a huge table with one row for each read classified.

Note that in most cases only the report, produced by running kraken2 with the --report otpion, is what you want. Then use the function kraken2_read_report.

Value

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

• status. C for classified reads, U for unclassified (if filter = TRUE only C).

• read_id. Short text identifying each read.

• name. Name of taxon, if classified.

• length. Length of read.

• tax_count. The k-mer counts for the read.

Author(s)

Lars Snipen.

See Also

kraken2_read_report.

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