I used the Megablast function (in the NGS: Mapping\ROCHE-454\) to
analyze my FASTA sequences against nt database and it worked fine for
me. However, it generated 56,804 hits although my query has only 1000
sequences. I am wondering is there any way to suppress the number of
reported alignments to just one best hit per sequence?   (In the local
BLAST there are parameters such as -K1 -v 1 -b 1 to do so, but I can't
find similar options in Galaxy).

Many thanks!

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