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Illumina sequencing instruments generate per-cycle BCL basecall files as primary sequencing output, but many downstream analysis applications use per-read FASTQ files as input. bcl2fastq combines these per-cycle BCL files from a run and translates them into FASTQ files. bcl2fastq can begin bcl conversion as soon as the first read has been completely sequenced.


To make bcl2fastq available, use the following module command in your submission scripts

module load apps/bcl2fastq/1.8.4

Installation Notes

These notes are primarily for system administrators.

Compilation was done using gcc 4.4.7. I tried it with gcc 4.8 but ended up with a lot of errors. The package is also dependent on Perl. Perl 5.10.1 was used which was the system Perl installed at the time. The RPM Perl-XML-Simple also needed installing.

export TMP=/tmp
export SOURCE=${TMP}/bcl2fastq
export BUILD=${TMP}/bcl2fastq-1.8.4-build
mkdir -p /usr/local/packages6/apps/gcc/4.4.7/bcl2fastq/1.8.4
export INSTALL=/usr/local/packages6/apps/gcc/4.4.7/bcl2fastq/1.8.4

mv bcl2fastq-1.8.4.tar.bz2 ${TMP}
cd ${TMP}
tar xjf bcl2fastq-1.8.4.tar.bz2

mkdir ${BUILD}
cd ${BUILD}
${SOURCE}/src/configure --prefix=${INSTALL}

make install