Scroll to navigation



fastaq_filter - Filter sequences to get a subset of them


usage: fastaq_filter [options] <infile> <outfile>

Filters a sequence file by sequence length and/or by name matching a regular expression

positional arguments:

Name of input file to be filtered
Name of output file


show this help message and exit
Minimum length of sequence to keep [0]
Maximum length of sequence to keep [inf]
If given, only reads with a name matching the regular expression will be kept
If given, only reads whose ID is in th given file will be used. One ID per line of file.
Only keep sequences that do not match the filters

Mate file for read pairs options:

Name of mates input file. If used, must also provide --mate_out
Name of mates output file
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