I am dealing with the blastn proctocal to scan the region without any homo information.
However, for those regions sharing huge homologous sequences, the blast will generate huge data and take a lot of time.
Therefore, I want to limit the output to those best hits, for example , top 20.
The command I used is as follows,
blastn -task blastn-short -db /data/WholeGenomeFasta/blast+/genome -query 1.fa -evalue 0.01 -num_threads 8 -outfmt "6 qseqid sseqid nident sstart send" -num_alignments 20
However, it seems that the parameter num_alignments did not work.
If there is any possible method I can do such a thing, and can I print the 20 alignments that sorted by the total identical counts?