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fastaq_filter - Filter sequences to get a subset of them

FASTAQ-FILTER(1) User Commands FASTAQ-FILTER(1)

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

optional arguments:

-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
June 2017 fastaq 3.15.0