FASTAQ-FILTER

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