Man page - fastaq-filter(1)
Packages contains this manual
- fastaq-filter(1)
- fastaq-version(1)
- fastaq-fasta_to_fastq(1)
- fastaq-split_by_base_count(1)
- fastaq-to_fasta(1)
- fastaq-translate(1)
- fastaq-reverse_complement(1)
- fastaq-add_indels(1)
- fastaq-to_tiling_bam(1)
- fastaq-acgtn_only(1)
- fastaq-trim_ends(1)
- fastaq-to_orfs_gff(1)
- fastaq-get_ids(1)
- fastaq-to_perfect_reads(1)
- fastaq-trim_contigs(1)
- fastaq-scaffolds_to_contigs(1)
- fastaq-search_for_seq(1)
- fastaq-to_mira_xml(1)
- fastaq-to_random_subset(1)
- fastaq-to_fake_qual(1)
- fastaq-sort_by_size(1)
- fastaq-merge(1)
- fastaq-enumerate_names(1)
- fastaq-strip_illumina_suffix(1)
- fastaq-to_boulderio(1)
- fastaq-caf_to_fastq(1)
- fastaq-count_sequences(1)
- fastaq-interleave(1)
- fastaq-make_random_contigs(1)
- fastaq-to_unique_by_id(1)
- fastaq-deinterleave(1)
- fastaq-replace_bases(1)
- fastaq-capillary_to_pairs(1)
- fastaq-sequence_trim(1)
- fastaq-sort_by_name(1)
- fastaq-expand_nucleotides(1)
- fastaq-chunker(1)
- fastaq-get_seq_flanking_gaps(1)
- fastaq(1)
apt-get install fastaq
Manual
FASTAQ-FILTER
NAMEDESCRIPTION
positional arguments:
options:
Mate file for read pairs options:
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