I would like to disable seeding when doing a sequence mapping using bwa.
Apparently, this is commonly performed using the aln -l option set at a
value higher than the read length, and is often set at values above 1000. In
Galaxy, the default option is -1 for this parameter, and it is indicated
that -1 corresponds to infinity. Does that mean that seeding can be disabled
using -1, and that it is disabled by default on Galaxy? I don't obtain
exactly the same thing using -1 or 16000 for this parameter, even though the
difference is marginal.


Thanks for your insights




Institut Jacques MONOD






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