Edit text on individual vs co-assembly

  - Remove 'Describe what de-replication is' from objectives; this is in the scope of the binning tutorial

Author: vinisalazar

topics/microbiome/tutorials/metagenomics-assembly/tutorial.md

@@ -12,7 +12,6 @@ questions:
   - "How to assess the quality of metagenomic data assembly?"
 objectives:
   - "Describe what an assembly is"
-  - "Describe what de-replication is"
   - "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"
@@ -169,11 +168,11 @@ In case of a not very large dataset it's more convenient to upload data directly
 
 As explained before, there are many challenges to metagenomics assembly, including:
 
-1. differences in coverage between samples, resulting from differences in abundance,
-2. the fact that different species often share conserved regions ({%cite kececioglu2001%}), and
-3. the presence of multiple strains of a single species ({%cite miller2010%}).
+1. Differences in coverage between samples, resulting from differences in abundance;
+2. The fact that different species often share conserved regions ({%cite kececioglu2001%}), and
+3. The presence of multiple strains of a single species ({%cite miller2010%}).
 
-To reduce the differences in coverage between samples, we can use a **co-assembly** approach, where reads from all samples are aligned together.:
+To reduce the differences in coverage between samples, we can use a **co-assembly** approach, where reads from all samples are aligned together:
 
 ![Image show one pile of sample1 reads and another pile of sample2 reads, then, green arrow leads to assembled reads from both piles](./images/co-assembly.png "Co-assembly"){:width="60%"}
 
@@ -195,11 +194,21 @@ In these cases, co-assembly is reasonable if:
 - Longitudinal sampling of the same site
 - Related samples
 
-If it is not the case, **individual assembly** should be prefered. In this case, an extra step of **de-replication** should be used:
+Examples where co-assembly would be reasonable:
+- Repeated sampling of the **same patient** along a particular amount of time.
+- Multiple samples taken from the **same site** and **similar environmental conditions**, eg. a patch of soil during the same sampling season.
+
+Examples where co-assembly would NOT be recommended:
+- Samples from different patients.
+- Samples from the same site, but over different seasons or under different environmental conditions, eg. a patch of soil before and after a bushfire event, a marine site under upwelling vs. under normal conditions.
+
+If samples differ like described, **individual assembly** is preferred. In the case of individual assembly, if **contigs are binned** after, an extra step of **de-replication** should be used:
 
 ![Image shows the process of individual assembly on two strains and five samples, after individual assembly of samples two samples are chosen for de-replication process. In parallel, co-assembly on all five samples is performed](./images/individual-assembly.png "Individual assembly followed by de-replication vs co-assembly. Source: dRep documentation"){:width="80%"}
 
-Co-assembly is more commonly used than individual assembly and then de-replication after binning. But in this tutorial, to show all steps, we will run an **individual assembly**.
+For more information on dereplication, check out the [metagenomic binning tutorial](../metagenomics-binning/tutorial.md).
+
+In this tutorial, to show all steps, we will run an **individual assembly**.
 
 > <comment-title></comment-title>
 > Sometimes it is important to run assembly tools both on individual samples and on all pooled samples, and use both outputs to get the better outputs for the certain dataset.
@@ -795,4 +804,4 @@ Once the choices made, metagenomic assembly can start:
 2. Assembly quality is evaluated with various metrics
 3. The assembly graph can be visualized.
 
-Once all these steps done, we can move to the next phase to build Metagenomics Assembled Genomes (MAGs): binning
+Once all these steps done, we can move to the next phase to build Metagenomics Assembled Genomes (MAGs): [metagenomic binning](../metagenomics-binning/tutorial.md).