BCL_convert is a tool for working with data generated by Illumina sequencing instruments. It is also the replacement for bcl2fastq which is no longer updated or supported by Illumina.
Roadmap for BCL_convert
Please note that we now recommend the use of the replacement Bioapps container image which includes BCL_convert and many more common bioinformatics tools and avoids the need for careful matching of dependencies between loaded software modules.
- The software can only be used "for the purpose of processing and analyzing data generated from an
Illumina genetic sequencing instrument owned and operated solely by (the University)"
- The software is only to be used for research purposes
- The software can only be used with data generated from the Illumina instrument, and not any data
generated from other sources
Load the module:
$ module load BCL-Convert
Run the software:
$ bcl-convert -h
bcl-convert Version 4.4.6
Copyright (c) 2014-2025 Illumina, Inc.
Run BCL Conversion (BCL directory to *.fastq.gz)
bcl-convert --bcl-input-directory <BCL_ROOT_DIR> --output-directory <PATH> [options]
Options:
-h [ --help ] Print this help message
-V [ --version ] Print the version and exit
--output-directory arg Output BCL directory for BCL conversion (must be specified)
-f [ --force ] Force: allow destination diretory to already exist
--bcl-input-directory arg Input BCL directory for BCL conversion (must be specified)
--sample-sheet arg Path to SampleSheet.csv file (default searched for in --bcl-input-directory)
--bcl-only-lane arg Convert only specified lane number (default all lanes)
--strict-mode arg Abort if any files are missing (false by default)
--first-tile-only arg Only convert first tile of input (for testing & debugging)
--tiles arg Process only a subset of tiles by a regular expression
--exclude-tiles arg Exclude set of tiles by a regular expression
--bcl-sampleproject-subdirectories arg Output to subdirectories based upon sample sheet 'Sample_Project' column
--sample-name-column-enabled arg Use sample sheet 'Sample_Name' column when naming fastq files &
subdirectories
--fastq-gzip-compression-level arg Set fastq output compression level 0-9 (default 1)
--shared-thread-odirect-output arg Use linux native asynchronous io (io_submit) for file output (Default=false)
--bcl-num-parallel-tiles arg # of tiles to process in parallel (default 1)
--bcl-num-conversion-threads arg # of threads for conversion (per tile, default # cpu threads)
--bcl-num-compression-threads arg # of threads for fastq.gz output compression (per tile, default # cpu
threads, or HW+12)
--bcl-num-decompression-threads arg # of threads for bcl/cbcl input decompression (per tile, default half # cpu
threads, or HW+8. Only applies when preloading files)
--bcl-only-matched-reads arg For pure BCL conversion, do not output files for 'Undetermined' [unmatched]
reads (output by default)
--run-info arg Path to RunInfo.xml file (default root of BCL input directory)
--no-lane-splitting arg Do not split FASTQ file by lane (false by default)
--create-fastq-for-index-reads arg
--num-unknown-barcodes-reported arg # of Top Unknown Barcodes to output (1000 by default)
--bcl-validate-sample-sheet-only arg Only validate RunInfo.xml & SampleSheet files (produce no FASTQ files)
--output-legacy-stats arg Also output stats in legacy (bcl2fastq2) format (false by default)
--bcl-enable-tile-metrics arg Output per-tile metrics in addition to aggregate (true by default)
--bcl-enable-adapter-cycle-metrics arg Output per-cycle adapter metrics in addition to aggregate (true by default)
--bcl-enable-detailed-demux-metrics arg Output demux error cycles and transitions (true by default)
--no-sample-sheet arg Enable legacy no-sample-sheet operation (No demux or trimming. No settings
supported. False by default, not recommended