NAME
kraken - assigning taxonomic labels to short DNA sequences
SYNOPSIS
kraken [options] <filename(s)>
OPTIONS
- --db NAME
-
Name for Kraken DB (default: none)
- --threads NUM
-
Number of threads (default: 1)
- --fasta-input
-
Input is FASTA format
- --fastq-input
-
Input is FASTQ format
- --gzip-compressed
-
Input is gzip compressed
- --bzip2-compressed
-
Input is bzip2 compressed
- --quick
-
Quick operation (use first hit or hits)
- --min-hits NUM
-
In quick op., number of hits req'd for classification NOTE: this is ignored if --quick is not specified
- --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
- --only-classified-output
-
Print no Kraken output for unclassified sequences
- --preload
-
Loads DB into memory before classification
- --paired
-
The two filenames provided are paired-end reads
- --check-names
-
Ensure each pair of reads have names that agree with each other; ignored if --paired is not specified
- --help
-
Print this message
- --version
-
Print version information
If none of the *-input or *-compressed flags are specified, and the file is a regular file, automatic format detection is attempted.