HPC:bclconvert

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BCL Convert

The Illumina BCL Convert is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina™ sequencing systems to FASTQ files. Additionally, BCL Convert provides adapter handling (through masking and trimming) and UMI trimming and produces metric outputs.

BCL Convert module usage

To check available versions of BCL Convert, run the "module avail" command (click "expand"):


[asrini@node155 ~]$ module avail

--------------------------------------------------------------------------------- /usr/share/Modules/modulefiles ----------------------------------------------------------------------------------
AllPaths-LG-v49967              bzip2/1.0.6                     gcc/8.3.1                       NAMD-2.9-Linux-x86_64-multicore R/3.1.1                         samtools-1.1
autoconf/2.69                   CASAVA/v1.8.2                   gsl-2.1                         ngsutils-0.5.7                  R/3.1.2                         scons/2.3.1
automake/1.15                   cellranger/5.0.1                hdf5/1.8.21                     null                            R/3.2.1                         SOAPdenovo2-r240
bamtools/2.3.0                  circos/0.67-5                   homer-v4.6                      pandoc/2.0.6                    R/3.2.2                         STAR/2.3.0e
bcftools/1.11                   cmake/3.21.1                    htslib/1.11                     pandoc/2.3                      R/3.3.0                         STAR/2.4.1d
bcl2fastq2/v2.15.0.4            cufflinks-2.2.0                 java/openjdk-1.6.0              parallel/20201122               R/3.3.1                         STAR/2.5.2a
bcl2fastq2/v2.16.0.10           cufflinks-2.2.1                 java/openjdk-1.7.0              pcre-8.38                       R/3.4.2                         STAR/2.7.1a
bcl2fastq2/v2.17.1.14           curl-7.49.0                     java/openjdk-1.8.0              perl5lib                        R/3.4.3                         texinfo/6.0
bcl2fastq2/v2.19.0.316          dot                             julia/1.0.5                     picard/1.96                     R/3.5.1                         texlive-20170214
bcl2fastq2/v2.20.0.422          EMBOSS-6.6.0                    julia/1.4.2                     picard-tools-1.141              R/3.6.3                         Trimmomatic-0.32
bcl-convert/3.8.2               eQtlBma-1.2.2                   ld-library-path                 pkg-config-path                 R/4.0.2                         trinity-r20140717
blat-v35                        eQtlBma-1.3.1                   libtool/2.4.6                   plink-1.90b3b                   rclone/1.47.0                   use.own
boost/1.55.0                    FastQC-0.11.2                   local_coreutils-8.24            python/2.7.9                    RUM/2.0.5_06                    wget/1.20.3
boost/1.57.0                    fastx_toolkit-0.0.14            manpath                         python/3.6.3                    sailfish/0.6.3                  WiggleTools/1.0
bowtie2/2.1.0                   gcc/5.3.1                       module-git                      python/3.9.1                    samtools/1.11                   zlib/1.2.8
bowtie2/2.3.4.1                 gcc/6.3.1                       module-info                     qiime/1.8.0                     samtools-0.1.18
bwa-0.7.10                      gcc/7.3.1                       modules                         QTLtools/1.3.1-11               samtools-0.1.19

---------------------------------------------------------------------------------------- /etc/modulefiles -----------------------------------------------------------------------------------------
mpi/mpich-3.0-x86_64 mpi/mpich-3.2-x86_64 mpi/mpich-x86_64

To load/use one of the available BCL Convert modules run the "module load" command (click "expand" to see basic module usage):


[asrini@node155 ~]$ module load bcl-convert/3.8.2 

[asrini@node155 ~]$ which bcl-convert
/opt/software/bcl-convert/3.8.2/bin/bcl-convert

[asrini@node155 ~]$ bcl-convert
bcl-convert Version 00.000.000.3.8.2-12-g85770e0b
Copyright (c) 2014-2018 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)
  --bcl-sampleproject-subdirectories arg Output to subdirectories based upon sample sheet 'Sample_Project' column
  --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)
  --no-lane-splitting arg                Do not split FASTQ file by lane (false by default)


[asrini@node155 ~]$ bcl-convert -V
bcl-convert Version 00.000.000.3.8.2-12-g85770e0b
Copyright (c) 2014-2018 Illumina, Inc. 

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