Option Description Default
--use-bases-mask
Specifies how to process each cycle:
• n—Ignore the cycle.
• Y (or y)—Use the cycle.
• I—Use the cycle for an Index Read.
• A number—Repeat the previous character the indicated number
of times.
• *—Repeat the previous character until the end of the read or index
(length per RunInfo.xml).
Commas separate read masks. The format for dual indexing is the
following syntax or specified variations:
--use-bases-mask Y*,I*,I*,Y*
You can also specify --use-bases-mask multiple times for separate
lanes. In the following example,1:indicates that the setting applies
to lane 1. The second --use-bases-mask parameter applies to all
other lanes.
--use-bases-mask 1:y*,i*,i*,y* --use-bases-mask
y*,n*,n*,y*
If this option is not specified, RunInfo.xml determines the mask. If it
cannot determine the mask, specify the --use-bases-mask option.
When specified, the number of index cycles and the index length in
the sample sheet must match.
N/A*
--with-failed-reads
Include all clusters in the output, including those that did not pass
filter. By default, clusters that did not pass filter are excluded.
FASTQ files containing failed reads cannot be uploaded to
BaseSpace Sequence Hub.
After cycle 25, RTA2 stops reading clusters that do not pass filter.
Systems other than MiSeq and HiSeq 2500 produce 25 bases, then
all Ns.
This option cannot be applied to CBCLfiles.
N/A*
--write-fastq-reverse-complement
Generate FASTQ files with the reverse complements of actual data. N/A*
--no-bgzf-compression
Turn off BGZF and use GZIP to compress FASTQ files.
BGZF compression allows downstream applications to decompress
in parallel. This option is available for FASTQ data consumers that
cannot handle standard GZIP formats.
N/A*
--fastq-compression-level
The Zlib compression level (1–9) to apply to FASTQ files. 4
--no-lane-splitting
Do not split FASTQ files by lane.
If you plan to upload the FASTQ files to BaseSpace Sequence Hub,
do not use
this option. It generates FASTQ files that are not
compatible with the file uploader.
N/A*
--find-adapters-with-sliding-window
Finds adapters using a simple sliding window algorithm. Ignores
adapter sequence indels.
N/A*
* Not applicable
General Options
General options determine miscellaneous settings for help, version information, and the minimum log level.
Option Description Default
-h,
--help
Produce a help message and exit the application. Not applicable
-v,
--version
Print version information. Not applicable
Document # 15051736 v03
For Research Use Only. Not for use in diagnostic procedures.
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bcl2fastq2 Conversion Software v2.20 Software Guide