Using DIAMOND with GV

Using DIAMOND with GV

Diamond is a faster alternative to BLAST and as such can be used to speed up a GeneValidator analysis.

Below is an example illustrating how Diamond output files can be passed to GeneValidator

# Install GV 
sh -c "$(curl -fsSL https://raw.githubusercontent.com/wurmlab/genevalidator/master/install.sh)"

cd genevalidator

# Install Diamond (see https://github.com/bbuchfink/diamond)
curl -L https://github.com/bbuchfink/diamond/releases/download/v2.1.6/diamond-linux64.tar.gz | tar -xz -C bin

# Make Diamond BLAST database 
diamond prepdb -d blast_db/swissprot

# Run BLASTP with Diamond
diamond blastp --db blast_db/swissprot --outfmt 5 --query exemplar_data/protein_data.fa --out exemplar_data/protein_data.xml

# Run GeneValidator with blastXML file produced 
genevalidator -n 8 -m 4 -d blast_db/swissprot -x exemplar_data/protein_data.xml exemplar_data/protein_data.fa