(see Figure 1) and specify options as described here. The default setting is applied if the option is not specified in the Demux section.

Note

The Demux section is optional and is intended for advanced users who have a good understanding of demultiplexing and filtering settings. For other users, do not add a Demux section and use the default demultiplexing settings.

Demultiplexing Option

Default

Description

filter-control-reads

Not present (false)

If flag is present, filter out reads marked as control reads in their FASTQ headers.

filter-failing-quality

Not present (false)

If flag is present, filter out reads marked as failing quality control in their FASTQ headers.

allowed-mismatches

3

The number of mismatches allowed, in total, between expected and observed index bases in order to match a read to a sample. Note that the default in the off-instrument demultiplexing software is 1 (see How Do I Demultiplex Off-instrument?).

min-delta

1

The minimum number of mismatches by which the best match for a read is better than the next-best match for a read in order to accept the best match. Note that the default in the off-instrument demultiplexing software is 2 (see How Do I Demultiplex Off-instrument?).

quality-mask-threshold

Not present

Mask to N template bases in all input reads whose base quality is below the specified value(s). If a single value is specified, it is applied to all input reads/FASTQs. If multiple values are provided in consecutive lines, then the first value applies to index 1, the second to index 2, the third to read 1, and the fourth to read 2. Note that sample barcode/index and UMI bases are never masked, even if a quality-mask-threshold is specified.

output-types

T

The types of bases/reads for which output files should be generated. A single string containing one or more of T (template), B (sample barcode), M (UMI), and S (skipped).

undetermined-sample-name

Undetermined

The name used as a prefix to generate FASTQ files for reads that did not match to any sample.

metric-prefix

N/A

Prepend this prefix to all output metric file names.

NOTE

If you use the template FlowCellTemplateDemuxFields.csv, make sure to review and edit the demultiplexing options. Some options need values in order for demultiplexing to work properly (allowed-mismatches, min-delta, quality-mask-threshold, output-types, undetermined-sample-name, and metric-prefix).