Comparative Genomics Exercise 0: Genome assembly and annotation

Login into the GDAV server

$ ssh youruser@IP

Create a directory in your home folder called compgenomics_ex1

$ mkdir compgenomics_ex0

and Enter the directory

$ cd compgenomics_ex0

All the files needed for this exercise are copied in the GDAV server at /home/compgenomics/assembly/. Make sure you can see them and take a few seconds to understand what they contain.

Tools needed

(already installed in the GDAV server)

• Spades
• Prokka
• bwa

Exercise

Goal 1 (Loxodonta orthologs)

Using the program spades, run a basic assembly and ORF prediction out of the two fastq files in /home/compgenomics/assembly.

Protocol

1. Run assembly:

$ spades.py -1 /home/compgenomics/assembly/SRR292770_1.fastq.gz -2 /home/compgenomics/assembly/SRR292770_2.fastq.gz -o my_assembly

2. Annotate ORFs and other elements with Prokka.

Use prokka, get a list of predicted genes in your assembly.

conda activate roary
$ prokka my_assembly/scaffolds.fasta

3. Map reads back to the assembly and genes.

bwa index scaffolds.fasta
bwa mem scaffolds.fasta /home/compgenomics/assembly/SRR292770_1.fastq.gz /home/compgenomics/assembly/SRR292770_2.fastq.gz > SRR292770.sam