fastaq-filter1
Filter sequences to get a subset of them
Overview
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
Releases
5 releases since Debian 9 (Stretch); the text changed 4 times.