blastn Command Examples

Nucleotide-Nucleotide BLAST. More information: https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.blastn_application_options/.

blastn -query {{query.fa}} -subject {{subject.fa}} -evalue {{1e-9}}

blastn -task blastn -query {{query.fa}} -subject {{subject.fa}}

blastn -query {{query.fa}} -subject {{subject.fa}} -outfmt {{'6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident'}} -out {{output.tsv}}

blastn -query {{query.fa}} -db {{path/to/blast_db}} -num_threads {{16}} -max_target_seqs {{10}}

blastn -query {{query.fa}} -db {{nt}} -remote

blastn -h