Command Line Options

--enable-kmer-classifier

Enables the Kmer Classifier. The default value is false

--output-file-prefix

Prefix for all output files for the classifier

--output-directory

Directory for all output files

--kmer-classifier-input-read-file

Input sequence file (zipped or unzipped) to the Kmer Classifier

--kmer-classifier-db-file

Database of sequences to classify against

--intermediate-reuslts-dir

Optional Area for temporary files. Size must be greater than size of all FASTQ files multiplied by 2

--kmer-classifier-load-db-ram

Optional Load the database onto RAM. Do not use if database in on ramdisk. The default value is false

--kmer-classifier-multiple-inputs

Optional Set to true to run with multiple inputs where input .tsv file has two columns: ID, Inputfile. The default value is false.

--kmer-classifier-min-window

Optional The minimum number of consecutive kmers for classify assignment at taxid. The default value is 1

--kmer-classifier-output-read-seq

Optional Enable a read sequence column in the output file. The default value is false.

--kmer-classifier-output-taxid-seq

Optional Enable a taxid string column in the output file. The default value is false.

--kmer-classifier-db-to-taxid-json

Optional Path to JSON file that maps database IDs to external taxids, names, and ranks

--kmer-classifier-no-read-output

Optional Do not create an individual read output. The default value is false

--kmer-classifier-no-taxid-counts

Optional Do not write a taxid count output file. The default value is false

--kmer-classifier-protein-input

Optional Indicate protein query sequences and database. The default value is false

--kmer-classifier-reads-to-keep

Optional Path to file of read IDs to use in alignment with one read per line

--kmer-classifier-no-remove-dups

Optional Do not deduplicate reads in input files

--kmer-classifier-ncpus

Optional Set the number of CPUs available for processing