Testing BUSCO phylogeny on a subset of Pseudomonas spp. genomes.
Make directory for analysis and move into it.
mkdir ~/scratch/pseudomonas
cd ~/scratch/pseudomonas
Make a file for the GenBank references of the required genomes and paste in the list of references and species names so that each is on a new line.
nano genomes.list
cat genomes.list
GCA_002905875.2 P_amygdali
GCA_002905795.2 P_avellanae
GCA_000007565.2 P_putida
GCA_000012205.1 P_savastanoi
GCA_000007805.1 P_syringae
GCA_000012245.1 P_syringae
GCA_002905835.1 P_syringae
GCA_900184295.1 P_viridiflava
Read line by line through genomes.list file and recursively download genomes from NCBI.
conda activate ncbi_datasets
cat genomes.list | while read REF SPECIES;
do datasets download genome accession $REF --filename $REF.zip
done
Unzip (and then delete zip files), rename and copy genomes to a new folder.
for file in *zip; do unzip -o $file; done
rm *zip
mkdir busco
cat genomes.list | while read REF SPECIES;
do cp ncbi_dataset/data/$REF/$REF*fna busco/"$REF"_"$SPECIES".fasta
done
Run BUSCO submission script on genomes.
cd busco
for file in *fasta;
do sbatch ../scripts/busco_bacteria.sh $file
done
Using BUSCO phylogenomics pipeline generate concatenated protein alignment of shared BUSCOs and plot tree.
cd ..
sbatch scripts/busco_phylo.sh busco/
Download tree file SUPERMATRIX.phylip.treefile and view in iTOL.