Blasting with DIAMOND

Make a new directory for diamond:

cd
mkdir diamond
cd diamond

Download diamond:

wget http://github.com/bbuchfink/diamond/releases/download/v0.7.9/diamond-linux64.tar.gz
tar xzf diamond-linux64.tar.gz

Put diamond in your path:

export PATH=$PATH:$HOME/diamond
echo 'export PATH=$PATH:$HOME/diamond' >> ~/.bashrc

Download the swissprot database:

wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
gunzip uniprot_sprot.fasta.gz

Index the database:

diamond makedb --in  uniprot_sprot.fasta -d  uniprot_sprot

Link in the fasta:

ln -s /salmon/nema_inList.fa
mkdir ./tempDir

Run Diamond:

diamond  blastx -d uniprot_sprot -q /mnt/data/nema_inList.fa -a matches -t tempDir -p 16

Convert to blast tab-separated output format:

diamond view -a matches.daa -o matches.m8

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