HPC:bclconvert
From HPC wiki
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" to see basic module usage):
[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):
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