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