bcl2fastq.py - Wrapper that outputs fastq files from bcl files

Tags

BCL FASTQ Conversion

Purpose

Convert the raw data from an Illumina Sequencing Run to fastq formatted files.

Usage

Example:

python bcl2fastq.py -p "--runfolder-dir <RunFolder>"

This command demultiplexes and converts BCL files in the given run folder directory. All arguments for Illumina’s bcl2fastq software must be given with the -p argument. Type:

python bcl2fastq.py --help

for command line help.

Documentation

Converts BCL files in a given run folder to fastq.

Command line options

--arguments

Supply arguments to be passed to Illumia’s bcl2fastq software.

--output-dir

Required if using –fastqc.

--fastqc

After converting BCL files, run all fastq files in FastQC.

--fastqc-options

Supply arguments to be passed to FastQC.

--bcl2fastq-help

Prints help for Illumina’s bcl2fastq software.

usage: bcl2fastq [-h] [-p ARGUMENTS] [-o OUTPUT] [-f] [-F FASTQC_OPTIONS] [-H]
                 [--timeit TIMEIT_FILE] [--timeit-name TIMEIT_NAME]
                 [--timeit-header] [--random-seed RANDOM_SEED] [-v LOGLEVEL]
                 [--log-config-filename LOG_CONFIG_FILENAME]
                 [--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
                 [-E STDERR] [-S STDOUT]
bcl2fastq: error: argument -?: expected one argument