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:

       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_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