adding assembly

Author: linsalrob

Workshops/INRB2023.md

@@ -156,3 +156,37 @@ In the above example, we started with two fastq files, removed adapter sequences
 We can combine all of that into a single `snakemake` file, and it will do all of the steps for us.
 
 See the [Snakemake](../Snakemake) section for details on how to run these two commands in a single pipeline.
+
+
+# Sequence Assembly
+
+See the [Sequence Assembly](../SequenceAssembly) section for a discussion of current sequence assemblers.
+
+To assemble the reads from the CF patient, we can install [spades](https://cab.spbu.ru/software/spades/). Here is the [spades manual](https://cab.spbu.ru/files/release3.15.4/manual.html) 
+
+```
+mamba install -y spades
+```
+
+or, if you did not install mamba, you can use
+
+```
+conda install -y spades
+```
+
+
+Then, we can assemble the filtered bacterial sequences using spades:
+
+```
+spades.py --meta -1 not_human/788707_20180129_S_R1.fastq.gz -2 not_human/788707_20180129_S_R2.fastq.gz -o not_human_assembly
+```
+
+Once you have assembled the sequences, the first step is to visualise the assembly with [bandage](https://rrwick.github.io/Bandage/).
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