NAME
fastaq_filter - Filter sequences to get a subset of them
DESCRIPTION
usage: fastaq_filter [options] <infile> <outfile>
Filters a sequence file by sequence length and/or by name matching a regular expression
positional arguments:
- infile
-
Name of input file to be filtered
- outfile
-
Name of output file
options:
- -h, --help
-
show this help message and exit
- --min_length INT
-
Minimum length of sequence to keep [0]
- --max_length INT
-
Maximum length of sequence to keep [inf]
- --regex REGEX
-
If given, only reads with a name matching the regular expression will be kept
- --ids_file FILENAME
-
If given, only reads whose ID is in th given file will be used. One ID per line of file.
- -v, --invert
-
Only keep sequences that do not match the filters
Mate file for read pairs options:
- --mate_in FILENAME
-
Name of mates input file. If used, must also provide --mate_out
- --mate_out FILENAME
-
Name of mates output file
- --both_mates_pass
-
By default, if either mate passes filter, then both reads output. Use this flag to require that both reads of a pair pass the filter