annotation.yml

id: annotation
title: Genome annotation
tabs:
  - id: tools
    title: Tools
    heading_html: >
      Common tools are listed here, or search for more in the full tool panel to the left.
    content:
      - title_html: <code>MAKER</code> - genome annotation pipeline
        description_html: >
          <p>
            MAKER is able to annotate both prokaryotes and eukaryotes. It works by aligning as many evidences as possible along the genome sequence, and then reconciling all these signals to determine probable gene structures.
            <br><br> The evidences can be transcript or protein sequences from the same (or closely related) organism. These sequences can come from public databases (like NR or GenBank) or from your own experimental data (transcriptome assembly from an RNASeq experiment for example). MAKER is also able to take into account repeated elements.
          </p>
        inputs:
          - datatypes:
              - fasta
            label: Genome assembly
          - datatypes:
              - fasta
            label: Protein evidence (optional)
        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmaker%2Fmaker"
      - title_html: <code>Funannotate predict</code> - predicted gene annotations
        description_html: >
          <p>
            <code>Funannotate predict</code> performs a comprehensive whole genome gene prediction. Uses AUGUSTUS, GeneMark, Snap, GlimmerHMM, BUSCO, EVidence Modeler, tbl2asn, tRNAScan-SE, Exonerate, minimap2. This approach differs from Maker as it does not need to train <em>ab initio</em> predictors.
          </p>
        inputs:
          - datatypes:
              - fasta
            label: Genome assembly (soft-masked)
          - datatypes:
              - bam
            label: Mapped RNA evidence (optional)
          - datatypes:
              - fasta
            label: Protein evidence (optional)
        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffunannotate_predict%2Ffunannotate_predict"
      - title_html: <code>RepeatMasker</code> - screen DNA sequences for interspersed repeats and low complexity regions
        description_html: >
          <p>
            RepeatMasker is a program that screens DNA for repeated elements such as tandem repeats, transposons, SINEs and LINEs. Galaxy AU has installed the full and curated DFam screening databases, or a custom database can be provided in <code>fasta</code> format. Additional reference data can be downloaded from <a href="https://www.girinst.org/repbase/" target="_blank"> RepBase</a>.
          </p>
        inputs:
          - datatypes:
              - fasta
            label: Genome assembly
        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Frepeat_masker%2Frepeatmasker_wrapper"
      - title_html: <code>InterProScan</code> - Scans InterPro database and assigns functional annotations
        description_html: >
          <p>
            Interproscan is a batch tool to query the InterPro database. It provides annotations based on multiple searches of profile and other functional databases.
          </p>
        inputs:
          - datatypes:
              - fasta
            label: Genome assembly
        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Finterproscan%2Finterproscan"
      - title_html: <code>Funannotate compare</code> - compare several annotations
        description_html: >
          <p>
            <code>Funannotate compare</code> compares several annotations and outputs a GFF3 file with the best gene models. It can be used to compare the results of different gene predictors, or to compare the results of a gene predictor with a reference annotation.
          </p>
        inputs:
          - datatypes:
              - fasta
            label: Genome assemblies to compare
        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffunannotate_compare%2Ffunannotate_compare"
      - title_html: <code>JBrowse</code> - Genome browser to visualize annotations
        description_html: ''
        inputs:
          - datatypes:
              - fasta
            label: Genome assembly
          - datatypes:
              - gff
              - gff3
              - bed
            label: Annotations
          - datatypes:
              - bam
            label: Mapped RNAseq data (optional)
        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fjbrowse%2Fjbrowse"
      - title_html: <code>Prokka</code> - Genome annotation, prokaryotes only
        description_html: ''
        inputs:
          - datatypes:
              - fasta
            label: Genome assembly
        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fcrs4%2Fprokka%2Fprokka"
  - id: workflows
    title: Workflows
    heading_html: >
      A workflow is a series of Galaxy tools that have been linked together to perform a specific analysis. You can use and customize the example workflows below.
      <a href="https://galaxyproject.org/learn/advanced-workflow/" target="_blank">Learn more.</a>
    content:
      - title_html: Annotation with Maker
        description_html: >
          <p>
            Annotates a genome using multiple rounds of Maker, including gene prediction using SNAP and Augustus. <br> <br> Tools: <code>maker</code> <code>snap</code> <code>augustus</code> <code>busco</code> <code>jbrowse</code>
          </p>
        inputs:
          - datatypes:
              - fasta
            label: Genome assembly
          - datatypes:
              - fastq
            label: RNAseq Illumina reads
          - datatypes:
              - fasta
            label: Proteins
        button_link: "{{ galaxy_base_url }}/u/anna/w/genome-annotation-with-maker"
        view_link: ''
        view_tip: ''
        button_tip: Run in Galaxy AU
      - title_html: Annotation with Funannotate
        description_html: >
          <p>
            Annotates a genome using Funannotate, includes RNAseq data with RNAstar, and protein predictions from EggNOG. <br> <br> Tools: <code>RNAstar</code> <code>funannotate</code> <code>eggnog</code> <code>busco</code> <code>jbrowse</code> <code>aegean parseval</code>
          </p>
        inputs:
          - datatypes:
              - fasta
            label: Genome assembly (soft-masked)
          - datatypes:
              - fastq
            label: RNAseq Illumina reads
          - datatypes:
              - gff3
            label: Alternative annotation
          - datatypes:
              - gbk
            label: Alternative annotation
        button_link: "{{ galaxy_base_url }}/u/anna/w/annotation-funannotate"
        view_link: ''
        view_tip: ''
        button_tip: Run in Galaxy AU
  - id: help
    title: Help
    content:
      - title_html: What is genome annotation?
        description_html: >
          <p>
            These <a href="https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/introduction/slides.html#1" target="_blank">slides</a> from the Galaxy training network explain the process of genome annotation in detail. You can use the <code style="font-size: 1.5rem;">&larr;</code> and <code style="font-size: 1.5rem;">&rarr;</code> keys to navigate through the slides.
          </p>
      - title_html: Genome annotation overview
        description_html: >
          <p>
            The flowchart below shows how you might use your input data (in green) with different Galaxy tools (in blue) to annotate a genome assembly. For example, one pathway would be taking an assembled genome, plus information about repeats, and data from RNA-seq, to run in the Maker pipeline. The annotatations can then be viewed in JBrowse.
          </p>
          <img class="img-fluid" src="/static/home/labs/genome/static/annotation-overview.png" alt="Genome annotation flowchart">
          <p class="text-center">
            A graphical representation of genome annotation
          </p>
      - title_html: Can I use Fgenesh++ for annotation?
        description_html: >
          <p>
            <a href="http://www.softberry.com/berry.phtml?group=help&subgroup=pipelines&topic=fgenesh_plus_plus" target="_blank"> Fgenesh++ </a> is a bioinformatics pipeline for automatic prediction of genes in eukaryotic genomes. It is presently not installed in Galaxy Australia, but the Australian Biocommons and partners have licensed the software and made it available via commandline. Australian researchers can apply for access through the Australian BioCommons.
          </p>
        button_html: Apply
        button_link: https://www.biocommons.org.au/fgenesh-plus-plus
        button_tip: Apply for access to Fgenesh++
      - title_html: Can I use Apollo to share and edit the annotated genome?
        description_html: >
          <p>
            Apollo is web-browser accessible system that lets you conduct real-time collaborative curation and editing of genome annotations.
          </p>
          <p>
            The Australian BioCommons and our partners at QCIF and Pawsey provide a hosted <a href="https://apollo-portal.genome.edu.au/" target="_blank"> Apollo Portal service </a> where your genome assembly and supporting evidence files can be hosted. All system administration is taken care of, so you and your team can focus on the annotation curation itself.
          </p>
          <p>
            This <a href="https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo-euk/tutorial.html" target="_blank"> Galaxy tutorial </a> provides a complete walkthrough of the process of refining eukaryotic genome annotations with Apollo.
          </p>
        button_html: More info
        button_link: https://support.biocommons.org.au/support/solutions/articles/6000244843-apollo-for-collaborative-curation-and-editing
      - title_html: Tutorials
        description_html: >
          <p class="lead">
            Genome annotation with Maker
          </p>
          <p>
            Genome annotation of eukaryotes is a little more complicated than for prokaryotes: eukaryotic genomes are usually larger than prokaryotes, with more genes. The sequences determining the beginning and the end of a gene are generally less conserved than the prokaryotic ones. Many genes also contain introns, and the limits of these introns (acceptor and donor sites) are not highly conserved. This <a href="https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html" target="_blank"> Galaxy tutorial </a> uses MAKER to annotate the genome of a small eukaryote: Schizosaccharomyces pombe (a yeast).
          </p>
          <hr>
          <p class="lead">
            Genome annotation with Funannotate
          </p>
          <p>
            This <a href="https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/funannotate/tutorial.html" target="_blank"> Galaxy tutorial </a> provides a complete walkthrough of the process of annotation with Funannotate, including the preparation of RNAseq data, structural annotation, functional annotation, visualisation, and comparing annotations.
          </p>
      - title_html: Galaxy Australia support
        description_html: >
          <p>
            Any user of Galaxy Australia can request support through an online form.
          </p>
        button_html: Request support
        button_link: /request/support