- Go to assembly page on NCBI. How many assembled genomes are available for S. aureus on GenBank and RefSeq?
- Go to the genome page of S. aureus and then press on Genome Assembly and Annotation report and then search for strain N315. Press on the accession number NC_002745.2 (GCF_000009645.1). Now let's try to download a fasta file*. Press on send to and then select file and then select fasta. This should download the fasta file. Do the same step but for strain Newman (NC_009641.1; GCF_000010465.1).
*Optionally, use ncbi-datasets to download both genomes right from the command line:
datasets download genome accession GCF_000009645.1 GCF_000010465.1
- Move these two files to MGJW
- Make a nucleotide blast database of both files. Check the name of the files and then concatenate them similar to the commands below. You will need to modify these commands based on the files' names.
conda activate blast
cat genome3.fasta genome4.fasta > genomes_3_4_combined.fasta
makeblastdb -in genomes_3_4_combined.fasta -title two_staph_blast_db -dbtype nucl
blastn -query Two_genes.fasta -db genomes_3_4_combined.fasta -outfmt '6 qseqid sacc evalue qcovs pident' -out Two_genes_output.txt
less Two_genes_output.txt
Let's type a S. aureus genome!
conda activate mlst
cd ~/MGJW/problem_set4/abricate_genomes
mlst --scheme saureus genome3.fasta
What is the Sequence Type (ST) of this genome?
You can also run mlst with multiple genomes at once using the *. When using *, make sure that all of the input files are assemblies as mlst works only with contig files.
Additionally, you can redirect the output of the above command to a new file instead of printing it to the screen. This is useful when you are working with many isolates and/or need the report for downstream processing. Let's try it:
mlst abricate_genomes/*.fasta > mlst_report.tsv
Let's take a look at the report:
less mlst_report.tsv
You will need to install Snippy for Session 6.
mamba create -n snippy -c bioconda snippy
conda activate snippy
snippy