Man page - fastaq-sequence_trim(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-SEQUENCE_TRIM
NAMEDESCRIPTION
positional arguments:
options:
NAME
fastaq_sequence_trim - Trim exact matches to a given string off the start of every sequence
DESCRIPTION
usage: fastaq_sequence_trim [options] <infile_1> <infile_2> <outfile_1> <outfile_2> <trim_seqs>
Trims sequences off the start of all sequences in a pair of sequence files, whenever there is a perfect match. Only keeps a read pair if both reads of the pair are at least a minimum length after any trimming
positional arguments:
infile_1
Name of forward fasta/q file to be trimmed
infile_2
Name of reverse fasta/q file to be trimmed
outfile_1
Name of output forward fasta/q file
outfile_2
Name of output reverse fasta/q file
trim_seqs
Name of file of sequences to search for at the start of each input sequence
options:
-h , --help
show this help message and exit
--min_length INT
Minimum length of output sequences [50]
--revcomp
Trim the end of each sequence if it matches the reverse complement. This option is intended for PCR primer trimming