Does anyone have any recommendations for
What aligners to use for long reads (e.g. Pac Bio, Oxford nanopore)?
Currently I am using gmap, blast, lastz, and blasr (I'm going to try out blat as well).
What particular parameters to use for these aligners to map long reads well.
For pac bio long reads I have been using gmap. In several presentations on oxford nanopore I have heard that they have used either blast or lastz to map reads. These programs have tons of parameters to tweak. I'd like to hear what some good choices are .
What aligners to use for long reads (e.g. Pac Bio, Oxford nanopore)?
Currently I am using gmap, blast, lastz, and blasr (I'm going to try out blat as well).
What particular parameters to use for these aligners to map long reads well.
For pac bio long reads I have been using gmap. In several presentations on oxford nanopore I have heard that they have used either blast or lastz to map reads. These programs have tons of parameters to tweak. I'd like to hear what some good choices are .
Comment