kraken

This group contains a single command that takes NCBI taxonomy .dmp files and kraken2 report files as inputs and generates a combined csv output with taxonomic information and read counts.

collect-reports

Aggregate kraken2 species classification report.

Given NCBI taxonomy database nodes.dmp file, names.dmp file, either a directory with Kraken2 classification results or a list of Kraken2 report files, aggregate all classification results into one file.

Options

option	description	required	default value
–nodes	NCBI taxonomy database nodes.dmp file	✓
–names	NCBI taxonomy database names.dmp file	✓
–out-csv	Output csv file name	✓
–kraken-dir	Directory containing kraken2 classification reports. Either –kraken-dir or reports as space separated arguments MUST be provided	✗
–pattern	Kraken report naming pattern. Used only if –kraken-dir is provided	✗	*.txt

Usage

using --kraken-dir

# using --kraken-dir
ngs-statter collect-reports --kraken-dir path/to/kraken_dir --out-csv path/to/reports.csv

using space separated kraken report files as arguments

# using space separated kraken report files as arguments
ngs-statter collect-reports --out-csv path/to/reports.csv path/to/report1.txt path/to/report2.txt