Perform sample demultiplexing on FASTQs.

Quick Start

$ pbrun demuxfastqs \
    --in-fq first.fq second.fq third.fastq \
    --metadata metadata.csv \
    --read-strucutres 7M1B+T 7M1B+T \
    --output-dir outputDir/

The --in-fq option takes one or more FASTQ files as input. The FASTQ filename must not start with a hyphen.

demuxfastqs Reference

Perform sample demultiplexing on FASTQs

Input/Output file options

--in-fq [IN_FQ [IN_FQ ...]]

Path to one or more fastq files each corresponding to a sub-read. Files can be in fastq or fastq.gz format. (default: None)

Option is required.

--metadata METADATA

Path to a file containing the metadata about the samples. If no file is provided, output reads will be put into unmatched files only. (default: None)

--out-dir OUT_DIR

Path to the directory that will contain all output files. (default: None)

Option is required.

Options specific to this tool

--read-structures [READ_STRUCTURES [READ_STRUCTURES ...]]

The read structure for each of the FASTQs. There must be one read structure per input fastq file. (default: None)

--out-metrics OUT_METRICS

The file to which per-barcode metrics are written in the output directory. If none given, a file named demux_barcode_metrics.txt will be written to the output directory. (default: None)


Remove the requirement that input read structures must contain sample barcodes. (default: None)

--num-threads NUM_THREADS

Number of worker threads. (default: 2)

Common options:

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)


Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.


Do not override seccomp options for docker (default: None).


View compatible software versions.


The --in-fq option takes the names of two FASTQ files. The FASTQ filenames must not start with a hyphen.