In order to polish my Falcon assembly of my D. suzukii genome, from PacBio long reads, I need to align the raw reads to my genome and create a .bam or a .sam file.
Such a tool already exist at PacBio, called blasr, but is currently not working (the 5.3 version I've installed do not provide a .bam or a .sam output... Which is VERY annoying).
Does an alternative of such aligner exist ? It has to be a aligner aware of the higher error rate of PacBio reads (that's why I can't use a classic aligner).
Any ideas ? I'm truely desesperate, I absolutely need to polish my assembly before going further in my analysis.
Thanks for your help !