Perform sample demultiplexing on FASTQs.
$ 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.
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)
- --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.