FASTAQ(1)                        User Commands                       FASTAQ(1)

       fastaq - FASTA and FASTQ file manipulation tools

       fastaq <command> [options]

       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

fastaq 3.17.0                      July 2018                         FASTAQ(1)