blastn

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