blastn:tldr:cae83

blastn: Align two or more sequences, custom tabular output format, output to file.

blastn

$ blastn -query ${query-fa} -subject ${subject-fa} -outfmt ${'6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident'} -out ${output-tsv}

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This command is using the blastn program to perform a nucleotide-nucleotide BLAST search. Here is a breakdown of the command:

blastn: This is the name of the program that will be used to perform the BLAST search.
-query ${query-fa}: This specifies the query sequence file in FASTA format. The ${query-fa} is a placeholder for the actual file path, which should be provided when running the command.
-subject ${subject-fa}: This specifies the subject sequence file in FASTA format. The ${subject-fa} is a placeholder for the actual file path, which should be provided when running the command.
-outfmt ${'6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident'}: This specifies the output format of the BLAST results. The ${'6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident'} is a placeholder for the desired output format, which includes various fields such as query sequence ID, query length, query start position, query end position, subject sequence ID, subject length, subject start position, subject end position, bit score, E-value, and percentage identity. The actual format specified must be provided when running the command.
-out ${output-tsv}: This specifies the output file path where the BLAST results will be saved. The ${output-tsv} is a placeholder for the actual file path, which should be provided when running the command. The results will be saved in tab-separated values (TSV) format.

Overall, this command is instructing the blastn program to perform a nucleotide BLAST search using a query sequence and a subject sequence, and generate an output file containing specific fields for each match found.

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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