Provided by: fastaq_3.17.0-1_all 
NAME
fastaq - FASTA and FASTQ file manipulation tools
SYNOPSIS
fastaq <command> [options]
DESCRIPTION0nf
To get minimal usage for a command use: fastaq command
To get full help for a command use one of: fastaq command -h fastaq command --help
Available commands:
acgtn_only Replace every non acgtnACGTN with an N add_indels Deletes or inserts
bases at given position(s) caf_to_fastq Converts a CAF file to FASTQ format capillary_to_pairs
Converts file of capillary reads to paired and unpaired files chunker Splits sequences
into equal sized chunks count_sequences Counts the sequences in input file deinterleave
Splits interleaved paired file into two separate files enumerate_names Renames sequences in a
file, calling them 1,2,3... etc expand_nucleotides Makes every combination of degenerate nucleotides
fasta_to_fastq Convert FASTA and .qual to FASTQ filter Filter sequences to get a
subset of them get_ids Get the ID of each sequence get_seq_flanking_gaps Gets the
sequences flanking gaps interleave Interleaves two files, output is alternating between
fwd/rev reads make_random_contigs Make contigs of random sequence merge Converts
multi sequence file to a single sequence replace_bases Replaces all occurrences of one letter
with another reverse_complement Reverse complement all sequences scaffolds_to_contigs Creates a
file of contigs from a file of scaffolds search_for_seq Find all exact matches to a string (and
its reverse complement) sequence_trim Trim exact matches to a given string off the start of
every sequence sort_by_name Sorts sequences in lexographical (name) order sort_by_size
Sorts sequences in length order split_by_base_count Split multi sequence file into separate files
strip_illumina_suffix Strips /1 or /2 off the end of every read name to_boulderio Converts to
Boulder-IO format, used by primer3 to_fake_qual Make fake quality scores file to_fasta
Converts a variety of input formats to nicely formatted FASTA format to_mira_xml Create an xml
file from a file of reads, for use with Mira assembler to_orfs_gff Writes a GFF file of open
reading frames to_perfect_reads Make perfect paired reads from reference to_random_subset
Make a random sample of sequences (and optionally mates as well) to_tiling_bam Make a BAM file
of reads uniformly spread across the input reference to_unique_by_id Remove duplicate sequences,
based on their names. Keep longest seqs translate Translate all sequences in input
nucleotide sequences trim_Ns_at_end Trims all Ns at the start/end of all sequences trim_contigs
Trims a set number of bases off the end of every contig trim_ends Trim fixed number of bases
of start and/or end of every sequence version Print version number and exit