My goal is to align my metagenomic sequences with virulence gene database in order to find out which probable genes are prevalent in the data.

So I ran diamond aligner using following commands:

1. diamond blastx -d nr.dmnd -q /home/DB04.fasta -o DB04_VG4 --evalue 0.00001 --id 25 --sensitive

2.diamond blastx -d nr.dmnd -q /home/DB04.fasta -o DB04_VG4 --evalue 0.001 --id 25 --sensitive

3.diamond blastx -d nr.dmnd -q /home/DB04.fasta -o DB04_VG4 --evalue 0.001 --id 25 --sensitive --query cover 40

4. diamond blastx -d nr.dmnd -q /home/DB04.fasta -o DB04_VG4 --evalue 0.001 --id 25 --sensitive --subject-cover 40

and few others.

Ofcourse, I am getting different numbers of genes with each command that I have used.

So I was just wondering which is the most reliable in predicting correct ones?

--sensitive is added due to long read sequencing

Or do I need to add some more parameters?

#bioinformatics #metagenomics #diamondalignment