Is getting the full query read as output from Blast possible?
If I understand the Blast manual correctly, the 'qseqid qseq' command will write the parts of the query sequence that match to a sequence in the database into the output. I would however like to get the whole query sequence. Is this possible, maybe with one of the length commands?
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The parts of the sequences you will see, in the alignments are defined by the query start/end positions, and the subject start/end positions. The length command specifies the min alignment length to report.
I don't think this is possible with BLAST itself. I do recall doing something similar with the
blastdbcmd. Can't help much more, but you might be able to track something down from there.