NAME
kraken2 - assigning taxonomic labels to short DNA sequences
SYNOPSIS
kraken2 [options] <filename(s)>
OPTIONS
- --db NAME
-
Name for Kraken 2 DB (default: none)
- --threads NUM
-
Number of threads (default: 1)
- --quick
-
Quick operation (use first hit or hits)
- --unclassified-out FILENAME
-
Print unclassified sequences to filename
- --classified-out FILENAME
-
Print classified sequences to filename
- --output FILENAME
-
Print output to filename (default: stdout); "-" will suppress normal output
- --confidence FLOAT
-
Confidence score threshold (default: 0.0); must be in [0, 1].
- --minimum-base-quality NUM
-
Minimum base quality used in classification (def: 0, only effective with FASTQ input).
- --report FILENAME
-
Print a report with aggregrate counts/clade to file
- --use-mpa-style
-
With --report, format report output like Kraken 1's kraken-mpa-report
- --report-zero-counts
-
With --report, report counts for ALL taxa, even if counts are zero
- --memory-mapping
-
Avoids loading database into RAM
- --paired
-
The filenames provided have paired-end reads
- --use-names
-
Print scientific names instead of just taxids
- --gzip-compressed
-
Input files are compressed with gzip
- --bzip2-compressed
-
Input files are compressed with bzip2
- --help
-
Print this message
- --version
-
Print version information
If none of the *-compressed flags are specified, and the filename provided is a regular file, automatic format detection is attempted.
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.