Read one or more Kraken2 sample reports

This function can read one or more Kraken(2) sample reports, as well as output of kraken2-inspect. Kraken2 reports with and without minimizer data are supported.

Usage

read_kraken_reports(files, minimizers, id = "file", num_threads = 1)

Arguments

files

Paths to files

minimizers

Boolean specifying whether the files include minimizer data

id

A string or NULL. If a string, create column with that name for storing the files or the names of the files vector

num_threads

Parameter passed onto readr::read_tsv()

Details

The column names in the resulting data frame are "clade_fragments_percent", "clade_fragments", "node_fragments", "minimizers_total", "minimizers_distinct", "rank_code", "taxid", "scientific_name"; the minimizer columns are only included if minimizers = TRUE.

This function should work on Kraken and Kraken2 reports as well as on the output of kraken2-inspect, but we've not tested it on original Kraken reports. Currently there is no check as to whether the minimizer data is in the reports or not; if minimizers is set incorrectly, the function will return without error but the reports will be parsed incorrectly.

• Kraken2 docs

• Kraken docs