DOKK / manpages / debian 11 / fastaq / fastaq-filter.1.en

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

April 2020

fastaq 3.17.0