blastn:tldr:036f3

blastn: 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

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

try on your machine

The command you provided is running the BLASTN tool, which is used for comparing nucleotide sequences against a database of nucleotide sequences.

Here is the breakdown of the command:

blastn: This is the command to run the BLASTN tool.
-query ${query-fa}: This specifies the query input file for BLASTN. The ${query-fa} is likely a placeholder that should be replaced with the actual file path of the query sequences in FASTA format.
-db ${path-to-blast_db}: This specifies the path to the BLAST database. The ${path-to-blast_db} is again a placeholder that should be replaced with the actual path to the BLAST database you want to search against.
-num_threads ${16}: This parameter defines the number of parallel threads to use for the search. The ${16} is a placeholder that should be replaced with the desired number of threads, in this case, 16.
-max_target_seqs ${10}: This parameter sets the maximum number of aligned sequences to keep from the database for each query sequence. The ${10} is a placeholder that should be replaced with the desired number of sequences, in this case, 10.

By executing this command with the appropriate file paths and values, BLASTN will be performed, comparing the query sequences in the specified file to the sequences stored in the BLAST database using 16 threads. It will retain a maximum of 10 aligned sequences from the database for each query sequence.

This explanation was created by an AI. In most cases those are correct. But please always be careful and never run a command you are not sure if it is safe.

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