ontology: EDAM (1.12)
topic:
  - Bioinformatics
scopes:
  - name: add_indels
    function:
     - Sequence mutation and randomization
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: caf_to_fastq
    function:
     - Formatting
    inputs:
     - data: Sequence assembly report
       formats:
       - CAF
    outputs:
     - data: Sequence
       formats:
       - FASTQ
  - name: capillary_to_pairs
    function:
     - Sequence file editing
    inputs:
     - data: Sequence
       formats:
       - FASTA
    outputs:
     - data: Sequence
       formats:
       - FASTA
  - name: chunker
    function:
     - Splitting
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: count_sequences
    function:
     - File handling
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: deinterleave
    function:
     - Splitting
    inputs:
     - data: Sequence
       formats:
       - FASTA
    outputs:
     - data: Sequence
       formats:
       - FASTA
  - name: enumerate_names
    function:
     - Sequence file editing
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: expand_nucleotides
    function:
     - Sequence generation (nucleic acid)
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: fasta_to_fastq
    function:
     - Formatting
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - qual
    outputs:
     - data: Sequence
       formats:
       - FASTQ
  - name: filter
    function:
     - Sequence file editing
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: get_ids
    function:
     - ID retrieval
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: get_seq_flanking_gaps
    function:
     - Sequence database search
    inputs:
     - data: Sequence
       formats:
       - FASTA
    outputs:
     - data: Sequence
       formats:
       - FASTA
  - name: interleave
    function:
     - Aggregation
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: make_random_contigs
    function:
     - Random sequence generation
    outputs:
     - data: Sequence
       formats:
       - FASTQ
  - name: merge
    function:
     - Aggregation
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: replace_bases
    function:
     - Sequence mutation and randomization
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: reverse_complement
    function:
     - Nucleic acid sequence reverse and complement
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: scaffolds_to_contigs
    function:
     - Sequence generation (nucleic acid)
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: search_for_seq
    function:
     - Sequence database search
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: sequence_trim
    function:
     - Sequence trimming
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: sort_by_size
    function:
     - Sequence file editing
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: split_by_base_count
    function:
     - Splitting
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: strip_illumina_suffix
    function:
     - Sequence file editing
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: to_fake_qual
    function:
     - Generation
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - qual
  - name: to_fasta
    function:
     - Formatting
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
       - GFF3-seq
       - EMBL format
       - GenBank forat
       - PHYLIP format
    outputs:
     - data: Sequence
       formats:
       - FASTA
  - name: to_mira_xml
    function:
     - Generation
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - XML
  - name: to_orfs_gff
    function:
     - Coding region prediction
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence features
       formats:
       - GFF3
  - name: to_perfect_reads
    function:
     - Generation
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTQ
  - name: to_random_subset
    function:
     - Random sequence generation
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTQ
  - name: to_tiling_bam
    function:
     - Generation
    inputs:
     - data: Sequence
       formats:
       - FASTA
    outputs:
     - data: Alignment
       formats:
       - BAM
  - name: translate
    function:
     - DNA translation
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
  - name: trim_Ns_at_end
    function:
     - Sequence trimming
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: trim_contigs
    function:
     - Sequence trimming
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
  - name: trim_ends
    function:
     - Sequence trimming
    inputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ
    outputs:
     - data: Sequence
       formats:
       - FASTA
       - FASTQ