A python script to use fastp to preprocess all FASTQ files within a folder. It will automatically couple the paired-end FASTQ files.
This script will generate an overall.html to present an aggregate summary for all processed FASTQ files.
python fastp.py -i /path/to/input/folder -o /path/to/output/folder -a '-f 3 -t 2'which means to
. process all the FASTQ data in the folder
. using fastp in PATH
. with arguments -f 3 and -t 3, which means trimming 3bp in head and 2bp in tail
. output all clean data and reports to another folder
Options:
--version show program's version number and exit
-h, --help show this help message and exit
-i INPUT_DIR, --input_dir=INPUT_DIR
the folder contains the FASTQ files to be
preprocessed, by default is current dir (.)
-o OUT_DIR, --out_dir=OUT_DIR
the folder to store the clean FASTQ. If not specified,
then there will be no output files.
-r REPORT_DIR, --report_dir=REPORT_DIR
the folder to store QC reports. If not specified, use
out_dir if out_dir is specified, otherwise use
input_dir.
-c COMMAND, --command=COMMAND
the path to fastp/fastplong command, if not specified,
then it will use 'fastp' in PATH
-a ARGS, --args=ARGS the arguments that will be passed to fastp. Enclose in
quotation marks. Like --args='-f 3 -t 3'
-p PARALLEL, --parallel=PARALLEL
the number of fastp processes can be run in parallel,
if not specified, then it will be CPU_Core/4
-1 READ1_FLAG, --read1_flag=READ1_FLAG
specify the name flag of read1, default is R1, which
means a file with name *R1* is read1 file
-2 READ2_FLAG, --read2_flag=READ2_FLAG
specify the name flag of read2, default is R2, which
means a file with name *R2* is read2 fileA python script to use fastplong to preprocess all FASTQ files within a folder. It will automatically couple the paired-end FASTQ files.
This script will generate an overall.html to present an aggregate summary for all processed FASTQ files.
python parallel.py -i /path/to/input/folder -o /path/to/output/folder -r /path/to/reports/folder -a '--cut_front --cut_tail'which means to
. process all the FASTQ data in /path/to/input/folder
. using fastplong in PATH
. the arguments --cut_front and --cut_tail will be passed to fastplong, to apply sliding window quality trimming from front and tail
. output all clean data to /path/to/output/folder
. output all HTML and JSON reports to /path/to/reports/folder
Options:
--version show program's version number and exit
-h, --help show this help message and exit
-i INPUT_DIR, --input_dir=INPUT_DIR
the folder contains the FASTQ files to be
preprocessed, by default is current dir (.)
-o OUT_DIR, --out_dir=OUT_DIR
the folder to store the clean FASTQ. If not specified,
then there will be no output files.
-r REPORT_DIR, --report_dir=REPORT_DIR
the folder to store QC reports. If not specified, use
out_dir if out_dir is specified, otherwise use
input_dir.
-c COMMAND, --command=COMMAND
the path to fastplong command, if not specified, then
it will use 'fastplong' in PATH
-a ARGS, --args=ARGS the arguments that will be passed to fastplong.
Enclose in quotation marks. Like --args='-f 3 -t 3'
-p PARALLEL, --parallel=PARALLEL
the number of fastplong processes can be run in
parallel, if not specified, then it will be CPU_Core/4