Bcl2fastq wrapper
Project description
bcl2fq-local
A bcl2fastq and qc wrapper
Install
pip install bcl2fq-local
or
git clone URL
cd bcl2fq-local
python setup.py install
Usage
For Bcl2fastq
usage: bcl2fq-local [-h] [-i DirPath] [-o DirPath] [--sample-sheet File] [--mismatch N] [--process N] [--io-process Num] [--binpath File] [--dry-run] [--mask MASK] [--mask-reads N] [--mask-index N] [-v] A bcl2fastq wrapper optional arguments: -h, --help show this help message and exit -i DirPath Sequence run dir -o DirPath Output dir for fastq files --sample-sheet File Using custom sample sheet file --mismatch N Mismatch for barcode, default: 1 --process N Process number for demultiplexing and processing --io-process Num Process number for reading and writing --binpath File bcl2fastq binary file path --dry-run Only print the cmd without running it --mask MASK using self defined mask --mask-reads N set reads mask base count, default is: 0,0 --mask-index N set index mask base count, default is: 0,0 -v, --version show version info
For QC
usage: qc-local [-h] [-r RAW_DIR] [-c CLEAN_DIR] [-q QC_DIR] [-2 ADAPTER_DIR] [-t THREADS] [--paired-end] [-v] A qc wrapper optional arguments: -h, --help show this help message and exit -r RAW_DIR Raw reads dir input -c CLEAN_DIR Dir to write output clean reads -q QC_DIR Dir to write qc info file, default: <clean_dir>/QC -2 ADAPTER_DIR Dir to write removed reads, default: <clean_dir>/002 -t THREADS Threads number for parallel, default:8 --paired-end Use qc for paired end reads -v, --version Show version info
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