Add figure of QUAST html report

Author: vinisalazar

topics/microbiome/tutorials/metagenomics-assembly/images/quast_html_report.png

@@ -15,7 +15,7 @@ objectives:
   - "Explain the difference between co-assembly and individual assembly."
   - "Explain the difference between reads, contigs and scaffolds."
   - "Explain how tools based on de Bruijn graph work."
-  - "Evaluate the Quality of the Assembly with QUAST, Bowtie2, and CoverM-Contig."
+  - "Evaluate the quality of the Assembly with QUAST, Bowtie2, and CoverM-Contig."
   - "Construct and apply simple assembly pipelines on short read data."
 time_estimation: "2H"
 key_points:
@@ -79,7 +79,7 @@ Assembling seems intuitively similar to putting together a jigsaw puzzle. Essent
 > 2. Overlap Layout Consensus
 > 3. De Bruijn graphs. The following figure illustrates these strategies in brief.
 >
-> ![Image shows greedy extention, overlap layout consensus, and de Brujin graphs assembly algorithms](./images/assembly-algorithms.png "Assembly algorithms. Image from {% cite carpentries %}"){:width="70%"}
+> ![Image shows greedy extention, overlap layout consensus, and de Brujin graphs assembly algorithms.](./images/assembly-algorithms.png "Assembly algorithms. Image from {% cite carpentries %}."){:width="70%"}
 >
 > The nice paper {% cite miller2010 %} on assemblers based on these algorithms will help you to better understand how they work.
 {: .details}
@@ -121,7 +121,7 @@ In case of a not very large dataset it's more convenient to upload data directly
 
 > <hands-on-title>Upload data into Galaxy</hands-on-title>
 >
-> 2. The information we need to import the samples for this tutorial (Sample ID, and link to the FASTQ file (URL) are in the grey box below.
+> - The information we need to import the samples for this tutorial (Sample ID, and link to the FASTQ file (URL) are in the grey box below.
 >
 >    ```text
 >    SampleID URL
@@ -147,15 +147,15 @@ In case of a not very large dataset it's more convenient to upload data directly
 >    - Paste the table.
 >    - Remove the first line.
 >    - Click **Build**
->    ![Rule-based Uploader](./images/data-import-1.png "Rule-based Uploader")
+>    ![Using the rule-based uploader.](./images/data-import-1.png "Using the rule-based uploader")
 >    - On the "Rules" pane on the left, click on "Click here" to set column definitions.
->    ![Column definitions](./images/data-import-2.png "Column definitions")
+>    ![Applying column definitions.](./images/data-import-2.png "Applying column definitions.")
 >    - Set the first column as "Name" and the second column as "URL".
->    ![Upload the data](./images/data-import-3.png "Upload the data")
+>    ![Uploading the data.](./images/data-import-3.png "Uploading the data.")
 >    - Click "Apply" and then "Upload".
 >
 >
-> 3. Create a paired collection named `Raw reads`, rename your pairs with the sample name
+> - Create a paired collection named `Raw reads`, rename your pairs with the sample name
 >
 >    {% snippet faqs/galaxy/collections_build_list_paired.md %}
 >
@@ -272,7 +272,7 @@ Contrary to **MetaSPAdes**, **MEGAHIT** does not output **scaffolds**. **Scaffol
 > {: .hands_on}
 {: .comment}
 
-> <question-title></question-title>
+> <question-title>Contig metrics</question-title>
 >
 > 1. How many contigs has been for ERR2231568 sample?
 > 2. And for ERR2231572?
@@ -289,15 +289,13 @@ Contrary to **MetaSPAdes**, **MEGAHIT** does not output **scaffolds**. **Scaffol
 {: .question}
 
 > <details-title>Co-assembly with MetaSPAdes</details-title>
+> MetaSPAdes supports co-assembly by passing a list of paired-end read files. MEGAHIT, on the other hand, requires concatenating that list of paired-end read files into a single pair of forward and reverse files.
 >
-> > <hands-on-title>Assembly with MetaSPAdes</hands-on-title>
-> >
-> > 1. {% tool [MetaSPAdes](toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.2.0+galaxy0) %} with following parameters
-> >    - *"Pair-end reads input format"*: `Paired-end: list of dataset pairs`
-> >        - {% icon param-collection %} *"FASTQ file(s): collection"*: `Raw reads`
-> >     - *"Select k-mer detection option"*: `User specific`
-> >        - *"K-mer size values"*: `21,33,55,77`
-> {: .hands_on}
+> 1. {% tool [MetaSPAdes](toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.2.0+galaxy0) %} with following parameters
+>    - *"Pair-end reads input format"*: `Paired-end: list of dataset pairs`
+>        - {% icon param-collection %} *"FASTQ file(s): collection"*: `Raw reads`
+>     - *"Select k-mer detection option"*: `User specific`
+>        - *"K-mer size values"*: `21,33,55,77`
 {: .details}
 
 # Quality control of assembly
@@ -322,7 +320,8 @@ Assemblies can be evaluated with **metaQUAST** ({%cite mikheenko2016%}), the met
 >    - *"Type of assembly"*: `Metagenome`
 >    - *"Output files"*: `HTML report`, `PDF report`, `Tabular reports`, `Log file`, `Key metric summary (metagenome mode)`, `Krona charts (metagenome mode without reference genomes)`
 >
-> 2. Inspect the HTML reports
+> 2. Inspect the HTML reports:
+> ![Screenshot of QUAST HTML report](./images/quast_html_report.png)s
 {: .hands_on}
 
 > <comment-title></comment-title>
@@ -644,7 +643,7 @@ This viewer draws contigs ordered from longest to shortest. Let's inspect this v
 >
 > Open the Contig size viewer for ERR2231568 and define start as `0` and end as `500000`
 >
-> ![Image shows on the Icarus Contig size viewer for ERR2231568, with a zoom between 0 500000. Below the menu, the contigs are drawn from the longest on the left to the shortest on the right. Each contig is filled with a different color: green for correct, red for misassembled, etc. Below the contigs is dispayed a bar to navigate through the contigs](./images/ERR2231568-contig-size-viewer.png)
+> ![Image shows on the Icarus Contig Size Viewer for ERR2231568, with a zoom between 0 500000. Below the menu, the contigs are drawn from the longest on the left to the shortest on the right. Each contig is filled with a different color: green for correct, red for misassembled, etc. Below the contigs is dispayed a bar to navigate through the contigs](./images/ERR2231568-contig-size-viewer.png)
 >
 > 1. What is the color of the first contig? Why?
 > 2. What is the red contig?