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