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Sequencing Optional Arguments

The following arguments are optional additions to a Bases2Fastq execution command for sequencing. Arguments that affect run parameters default to the value that is recorded in the RunParameters.json file from the run.

--chemistry-version​

Use --chemistry-version to overwrite the sequencing kit version in RunParameters.json. Use on one of the following valid values:

  • Cloudbreak for a Cloudbreak kit
  • CloudbreakFS for a Cloudbreak Freestyle kit
  • CloudbreakUQ for a Cloudbreak UltraQ kit
  • Trinity for a Trinity kit
bases2fastq /input /output --chemistry-version <SEQ_KIT_VERSION>

--demux-only​

Use --demux-only or -d to enable demultiplexing-only mode, which performs demultiplexing and outputs index metrics without generating any FASTQ files.

bases2fastq /input /output --demux-only
bases2fastq /input /output -d

--detect-adapters​

Use --detect-adapters to detect adapter sequences and override any sequences present in the run manifest. For more information, see Adapter Trimming.

bases2fastq /input /output --detect-adapters

--error-on-missing​

Use --error-on-missing or -m to terminate an execution for a missing file. By default, missing files are skipped and execution continues.

bases2fastq /input /output --error-on-missing
bases2fastq /input /output -m

--exclude-tile​

Use --exclude-tile or -e to specify a subset of tiles to exclude from processing. The argument uses regex to identify the tiles. To specify multiple subsets, enter the argument multiple times.

bases2fastq /input /output --exclude-tile '<EXCLUSION_TILES_REGEX>'
bases2fastq /input /output -e '<EXCLUSION_TILES_REGEX>'

The following examples exclude the tiles from lane 1:

bases2fastq /input /output --exclude-tile 'L1R..C..S.'
bases2fastq /input /output -e 'L1R..C..S.'

--filter-mask​

Use --filter-mask to apply a custom base mask to specify the cycles that determine if a read passes filter. Separate each read section with a hyphen. The argument is only compatible with Cloudbreak or Cloudbreak Freestyle chemistry. The default values are R1:Y15N* and R2:Y15N*. In AVITI OS, the Filter Mask setting for the Advanced Run Settings add-on can modify the default values.

bases2fastq /input /output --filter-mask <FILTER_MASK>

The following example applies a filter mask with the base mask I1:Y4N*, which refers to the first four cycles of the Index 1 read:

bases2fastq /input /output --filter-mask I1:Y4N*

The following example applies a filter mask with the base masks R1:Y18N* and R2:Y18N*, which refer to the first 18 cycles of both Read 1 and Read 2.

bases2fastq /input /output --filter-mask R1:Y18N*-R2:Y18N*

--flowcell-id​

Use --flowcell-id to overwrite the flow cell ID in the RunParameters.json file with another flow cell ID. Also, you can use this argument to add a missing flow cell ID. Replace FLOWCELL_ID with your flow cell ID.

bases2fastq /input /output --flowcell-id <FLOWCELL_ID>

The following example updates the flow cell ID to 123abc123:

bases2fastq /input /output --flowcell-id <123abc123>

--force-index-orientation​

Use --force-index-orientation to perform demultiplexing without detecting the index sequence orientation. When used, Bases2Fastq applies the orientation that is recorded in the run manifest.

bases2fastq /input /output --force-index-orientation

--group-fastq​

Use --group-fastq to group all generated sample FASTQ files at the root of the project folder.

bases2fastq /input /output --group-fastq

When used with --no-projects, Bases2Fastq groups all generated sample FASTQ files in the Samples folder.

bases2fastq /input /output --group-fastq --no-projects

--help​

Use --help or -h to display the usage statement for Bases2Fastq.

bases2fastq --help
bases2fastq -h

--i1-cycles​

Use --i1-cycles to overwrite the number of cycles in Index 1 in RunParameters.json with another value.

bases2fastq /input /output --i1-cycles <NUMBER_OF_CYCLES>

--i2-cycles​

Use --i2-cycles to overwrite the number of cycles in Index 2 in RunParameters.json with another value.

bases2fastq /input /output --i2-cycles <NUMBER_OF_CYCLES>

--include-tile​

Use --include-tile or -i to specify a subset of tiles to include in the execution. To include specific tiles, you must exclude all tiles with the --exclude-tile or -e argument. The argument uses regex to identify the selected tiles. To specify multiple subsets, enter the argument multiple times.

bases2fastq /input /output --exclude-tile '<EXCLUSION_TILES_REGEX>' --include-tile '<INCLUSION_TILES_REGEX>'
bases2fastq /input /output -e '<EXCLUSION_TILES_REGEX>' -i '<INCLUSION_TILES_REGEX>' -i '<INCLUSION_TILES_REGEX>'

The following example includes the subset of tiles L1R..C..S2 after excluding all tiles:

bases2fastq /input /output --exclude-tile 'L.R..C..S.' --include-tile 1R..C..S2>'

The following example includes the additional subset of tiles L2R..C..S1:

bases2fastq /input /output -e 'L.R..C..S.' -i 'L1R..C..S2' -i 'L2R..C..S1'

--input-remote​

Use --input-remote to set the rclone remote name for the remote INPUT_DIRECTORY.

bases2fastq /input /output --input-remote <INPUT_DIRECTORY_NAME>

--kit-configuration​

Use --kit-configuration to overwrite the kit configuration in RunParameters.json. Use one of the following valid values:

  • 150Cycles for a 2 x 75 kit
  • 300Cycles for a 2 x 150 kit
  • 600Cycles for a 2 x 300 kit
bases2fastq /input /output --kit-configuration <KIT_CONFIGURATION>

--legacy-fastq​

Use --legacy-fastq to apply a legacy file naming convention to FASTQ files, such as SampleName_S1_L001_R1_001.fastq.gz. Some secondary analysis software might require this naming convention.

Note:  

The --legacy-fastq argument is not compatible with lane merging. When you use the --legacy-fastq argument, Bases2Fastq writes the FASTQ files as split lanes. Therefore, if you combine the --split-lanes and --legacy-fastq arguments, the --legacy-fastq argument takes precedence, and Bases2Fastq displays a warning message before proceeding with the execution.

bases2fastq /input /output --legacy-fastq

--log-level​

Use --log-level or -l to specify the minimum level required to log an event. The default value is INFO. Use one of the following valid values:

  • INFO
  • DEBUG
  • WARNING
  • ERROR
bases2fastq /input /output --log-level <MIN_LOG_LEVEL>
bases2fastq /input /output -l <MIN_LOG_LEVEL>

--no-error-on-invalid​

Use --no-error-on-invalid or -n to skip invalid files and continue execution. By default, missing files are skipped and execution continues.

bases2fastq /input /output --no-error-on-invalid
bases2fastq /input /output -n

--no-projects​

Use --no-projects to organize the output file directory without project folders into the standard, sample-based folder structure.

bases2fastq /input /output --no-projects

--num-threads​

Use --num-threads or -p to specify the number of threads to use for processing, with a minimum value of 1 and a maximum value that is based on your system. The default value is 1.

bases2fastq /input /output --num-threads <NUMBER_OF_THREADS>
bases2fastq /input /output -p <NUMBER_OF_THREADS>

The following example specifies 10 threads to use for processing:

bases2fastq /input /output --num-threads 10
bases2fastq /input /output -p 10

--num-unassigned​

Use --num-unassigned to specify a value that indicates the maximum number of unassigned sequences to support. The default value is 30. Unassigned sequences do not have a minimum required number of observations and are reported in descending order based on the polony count. A single polony might contribute to an unassigned sequence.

bases2fastq /input /output --num-unassigned <MAX_NUMBER_UNASSIGNED>

The following example specifies 35 as the maximum number of unassigned sequences to support:

bases2fastq /input /output --num-unassigned 35

--output-remote​

Use --output-remote to set the rclone remote name that points to the output files.

bases2fastq /input /output --output-remote <OUTPUT_DIRECTORY_NAME>

--preparation-workflow​

Use --preparation-workflow to overwrite the library prep workflow in RunParameters.json with one of the following valid values:

  • Adept
  • Elevate
  • ThirdParty
bases2fastq /input /output --preparation-workflow <LIBRARY_PREP_WORKFLOW>

--qc-only​

Use --qc-only to enable QC-only mode, which generates a representative view of run metrics on one tile and no FASTQ files. Executions in QC-only mode are faster than executions with demultiplexing and can support the following scenarios:

  • Troubleshooting parameters applied to execution
  • Troubleshooting execution issues for specific tiles
  • Quickly obtaining QC metrics for a run
bases2fastq /input /output --qc-only

You can use --include-tile to execute QC-only mode on more than one tile. The following example executes QC-only mode on all tiles in lane 1:

bases2fastq /input /output --qc-only --include-tile 'L1R..C..S.'

--r1-cycles​

Use --r1-cycles to overwrite the number of cycles for Read 1 in RunParameters.json with another value.

bases2fastq /input /output --r1-cycles <NUMBER_OF_CYCLES>

--r2-cycles​

Use --r2-cycles to overwrite the number of cycles for Read 2 in RunParameters.json with another value.

bases2fastq /input /output --r2-cycles <NUMBER_OF_CYCLES>

--run-manifest​

Use --run-manifest or -r to define the location of an alternate run manifest for the execution instead of the RunManifest.csv file output by the instrument. For more information on corrected run manifests, see the Run Manifest Documentation.

bases2fastq /input /output --run-manifest <PATH/TO/CORRECTED_MANIFEST.CSV>
bases2fastq /input /output -r <PATH/TO/CORRECTED_MANIFEST.CSV>

--settings​

Use --settings to overwrite run manifest settings. Entering the argument for each setting you want to overwrite. For more information on available settings, see the Run Manifest Documentation.

bases2fastq /input /output --settings '<SETTING_ARGUMENT>'

The following example changes the run manifest setting for generating an Index 1 FASTQ file to True:

bases2fastq /input /output --settings 'I1Fastq,True'

If you want to overwrite two different settings, you can use --settings twice. The following example also changes the Index 1 base mask to I1:N3Y*.

bases2fastq /input /output --settings 'I1Fastq,True' --settings 'I1Mask,I1:N3Y*'

--skip-multi-qc​

Use --skip-multi-qc to skip the creation of a multiQC report.

bases2fastq /input /output --skip-multi-qc

--skip-qc-report​

Use --skip-qc-report to skip the creation of an HTML QC report.

bases2fastq /input /output --skip-qc-report

--split-lanes​

Use --split-lanes to divide FASTQ files by flow cell lane.

Note:  

When you use the --legacy-fastq argument, Bases2Fastq writes the FASTQ files as split lanes. Therefore, if you combine the --split-lanes and --legacy-fastq arguments, the --legacy-fastq argument takes precedence, and Bases2Fastq displays a warning message before proceeding with the execution.

bases2fastq /input /output --split-lanes

--version​

Use --version or -v to display the current Bases2Fastq version. Bases2Fastq logs the version at the start of any execution on the command line and in the log file.

bases2fastq --version
bases2fastq -v
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