Alignment Parameters for Long Reads

[bdeonovic]

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 .

[Brian Bushnell]

These are the settings I've been using for evaluating Nanopore data with BBMap:

mapPacBio.sh k=8 in=reads.fq maxreadlen=1000 minlen=200 sam=1.4 idtag ow int=f qin=33 mhist=mhist1.txt idhist=idhist1.txt ehist=ehist1.txt indelhist=indelhist1.txt lhist=lhist1.txt gchist=gchist1.txt qhist=qhist1.txt qahist=qahist1.txt bhist=bhist1.txt out=mapped.sam minratio=0.15 ignorequality slow ordered maxindel1=80 maxindel2=800 outputunmapped=f bs=bs1.sh

BBMap currently supports a max read length of 6kbp, which is unfortunate, but it has higher sensitivity than most others. It's still clear in the output which reads mapped full-length; they are broken into pieces, but the pieces are adjacent in the sam file and have the same name (suffixed by _1, _2, _3, etc). I capped the read length at 1kbp for ONP data due to the bursty error model, but for Pac Bio reads, I cap it at 6kbp.