blastn

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

• 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