blastp:tldr:404b0
This command is using the program blastp to compare the sequences of two protein databases or files. Here is the explanation of each part of the command:
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blastp: This is the name of the Blast program to be used, which is specifically designed for comparing protein sequences.
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-query ${query-fa}: This specifies the file or database containing the query sequences for which you want to find matches. The ${query-fa} is a placeholder that should be replaced with the actual file name or path.
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-subject ${subject-fa}: This indicates the file or database containing the subject sequences against which you want to compare the query sequences. Similar to the previous option, ${subject-fa} should be replaced with the actual file name or path.
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-outfmt '${6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident}': This defines the output format of the Blast results. In this case, it specifies that we want to display the values of several fields for each alignment hit. The numbers after the $ symbol represent the indexes of the desired fields, and the field names (e.g., qseqid, qlen, etc.) indicate what information will be included in the output.
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-out ${output-tsv}: This specifies the file where the Blast results will be saved. Again, ${output-tsv} is a placeholder that needs to be replaced with the desired file name or path.
Overall, this command will perform a blastp comparison between the query and subject sequences, outputting specific fields of interest for each alignment hit in a tab-separated values (tsv) format into the specified output file.