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

fastaq 3.17.0                                     December 2024                                        FASTAQ(1)