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Bcl2Qseq – BCL to Qseq converter

The Seal bcl2qseq program uses your Hadoop cluster to extract reads in qseq format from an Illumina run directories. Internally it wraps Illumina’s own bclToQseq utility so it supports all the same features.

Since this program reads its input data directly from the run directory, the input data needs to be on a shared storage volume mounted at the same point on all the Hadoop nodes.

Bcl2Qseq will run one instance of Illumina’s bclToQseq per flowcell tile; thus, it will produce one output file per tile.


seal bcl2qseq [OPTIONS] /path/to/run/directory /path/to/output/dir

Command line options

Short Long Description
-l F

–logfile F

–bclToQseq-path P






Write log output to file F (default: stderr).

Complete path to Illumina’s bclToQseq utility, if it’s not in the PATH.

If your installation of bclToQseq needs addition library paths to run, you may provide a colon-separated list with this argument.

Ignore missing or corrupt bcl files (see Illumina’s bclToQseq documentation).

Ignore missing or corrupt control files (see Illumina’s bclToQseq documentation).

See Illumina’s bclToQseq documentation.

See Illumina’s bclToQseq documentation.

Configurable Properties

Bcl2Qseq does not have any program-specific configurable properties at the moment. You can still use its section to configure Hadoop property values specific to Bcl2Qseq.


Config File Section Title: None yet – TODO!