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