SYNOPSIS

fastaq ,<command> /[,options/]

DESCRIPTIONnf

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