Using BLAST+ for nucleotide alignments
It’s quite some time since I needed to run BLAST locally on anything. Here are some quick notes.
First download BLAST:
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.30+-x64-linux.tar.gz tar xvzf ncbi-blast-2.2.30+-x64-linux.tar.gz cd ncbi-blast-2.2.30+/bin
Create a new reference database:
./makeblastdb -in ~/genomics/myreference.fasta -dbtype nucl
In my case I needed to align fastq files. However BLAST only takes fasta. I used to the following to convert the fastqs to fastas:
awk 'BEGIN{n=0;}{if(n%4 == 0) print ">" substr($0,2); if(n%4 == 1) print $0;n++;}' input.fastq > output.fasta
And finally run the alignment:
./blastn -db ~/genomics/myreference.fasta -query ./output.fasta
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