table of contents
| 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:¶
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
| October 2022 | fastaq_filter 3.17.0 |