This is the command fastaq-filter that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use fastaq-filter online using onworks.net services
