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communities/microgalaxy/lab/sections/1_data_import_and_preparation.yml

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+id: data
+title: Data import and preparation
+tabs:
+  - id: tools
+    title: Tools
+    heading_md: >
+      Common tools are listed here, or search for more in the full tool panel to the left.
+    content:
+      - title_md: Import data to Galaxy
+        description_md: >
+          Standard upload of data to Galaxy, from your computer or from the web.
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1"
+      - title_md: <code>FastQC</code> - sequence quality reports
+        description_md: >
+          <p>
+            Before using your sequencing data, it's important to ensure that
+            the data quality is sufficient for your analysis.
+          </p>
+        inputs:
+          - datatypes:
+              - fastq
+              - bam
+              - sam
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc"
+      - title_md: <code>FastP</code> - sequence quality reports, trimming & filtering
+        description_md: >
+          <p>
+            Faster run than FastQC, this tool can also trim reads and filter by quality.
+          </p>
+        inputs:
+          - datatypes:
+              - fastq
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffastp%2Ffastp"
+      - title_md: <code>NanoPlot</code> - visualize Oxford Nanopore data
+        description_md: >
+          <p>
+            A plotting suite for Oxford Nanopore sequencing data and alignments.
+          </p>
+        inputs:
+          - datatypes:
+              - fastq
+              - fasta
+              - vcf_bgzip
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnanoplot%2Fnanoplot"
+      - title_md: <code>GenomeScope</code> - estimate genome size
+        description_md: >
+          <p>
+            A set of metrics and graphs to visualize genome size and complexity prior to assembly.
+          </p>
+        inputs:
+          - datatypes:
+              - tabular
+            label: Output from <code>Meryl</code> or <code>Jellyfish histo</code>
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgenomescope%2Fgenomescope"
+      - title_md: <code>Meryl</code> - count kmers
+        description_md: >
+          <p>
+            Prepare kmer count histogram for input to GenomeScope.
+          </p>
+        inputs:
+          - datatypes:
+              - fastq
+              - fasta
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmeryl%2Fmeryl"
+
+  - id: workflows
+    title: Workflows
+    heading_md: >
+      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_md: Data QC
+        description_md: >
+          <p>
+            Report statistics from sequencing reads. <br> <br> Tools: <code>nanoplot</code> <code>fastqc</code> <code>multiqc</code>
+          </p>
+        button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=222"
+        view_link: https://workflowhub.eu/workflows/222
+        view_tip: View in WorkflowHub
+        button_tip: Import to Galaxy AU
+      - title_md: Kmer counting to estimate genome size
+        description_md: >
+          <p>
+            Estimates genome size and heterozygosity based on counts of kmers. <br> <br> Tools: <code>meryl</code> <code>genomescope</code>
+          </p>
+        button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=223"
+        view_link: https://workflowhub.eu/workflows/223
+        view_tip: View in WorkflowHub
+        button_tip: Import to Galaxy AU
+      - title_md: Trim and filter reads
+        description_md: >
+          <p>
+            Trims and filters raw sequence reads according to specified settings. <br> <br> Tools: <code>fastp</code>
+          </p>
+        button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=224"
+        view_link: https://workflowhub.eu/workflows/224
+        view_tip: View in WorkflowHub
+        button_tip: Import to Galaxy AU
+
+  - id: tutorials
+    title: Tutorials
+    heading_md: >
+       
+    content: []
+
+  - id: faq
+    title: FAQ
+    heading_md: >
+       
+    content: []