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