usage: pyBioTools Fastq Filter [-h] -i [INPUT_FN [INPUT_FN ...]] -o OUTPUT_FN
[-l MIN_LEN] [-u MIN_QUAL] [-r]
[-f QUAL_OFFSET] [-v] [-q] [--progress]
Filter fastq reads based on their length, mean quality and the presence of
duplicates. Can also be used to concatenate reads from multiple files in a
single one.
optional arguments:
-h, --help show this help message and exit
-i [INPUT_FN [INPUT_FN ...]], --input_fn [INPUT_FN [INPUT_FN ...]]
Fastq file path or directory containing fastq files or
list of files, or regex or list of regex. It is quite
flexible. (required) [str]
-o OUTPUT_FN, --output_fn OUTPUT_FN
Destination fastq file. Automatically gzipped if the
.gz extension is found (required) [str]
-l MIN_LEN, --min_len MIN_LEN
Minimal reads length (default: None) [int]
-u MIN_QUAL, --min_qual MIN_QUAL
Minimal mean read PHRED quality (default: None)
[float]
-r, --remove_duplicates
If true duplicated reads with the same read id are
discarded (default: False) [None]
-f QUAL_OFFSET, --qual_offset QUAL_OFFSET
Quality scoring system off set. Nowadays pretty much
everyone uses +33 (default: 33) [int]
-v, --verbose Increase verbosity (default: False)
-q, --quiet Reduce verbosity (default: False)
--progress Display a progress bar
(pyBioTools)