blastn
Nucleotide-Nucleotide BLAST.
TLDR
Align two or more sequences using megablast (default), with the e-value threshold of 1e-9, pairwise output format (default)
$ blastn -query [query.fa] -subject [subject.fa] -evalue [1e-9]
Align two or more sequences using blastn
$ blastn -task blastn -query [query.fa] -subject [subject.fa]
Align two or more sequences, custom tabular output format, output to file
$ blastn -query [query.fa] -subject [subject.fa] -outfmt ['6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident'] -out [output.tsv]
Search nucleotide databases using a nucleotide query, 16 threads (CPUs) to use in the BLAST search, with a maximum number of 10 aligned sequences to keep
$ blastn -query [query.fa] -db [path/to/blast_db] -num_threads [16] -max_target_seqs [10]
Search the remote non-redundant nucleotide database using a nucleotide query
$ blastn -query [query.fa] -db [nt] -remote
Display help (use -help for detailed help)
$ blastn -h
