After error-correcting PacBio long reads using Illumina short-reads, what aligners are adept for aligning the corrected PacBio long reads against the genome?
Should I think of the corrected PacBio reads as just "long Illumina reads" (in terms of error & indel rate, etc.) ?
I am tempted to use BLASR, but the PacBio-specific error rates and indels are presumably "corrected out", so it still appropriate to use BLASR?
Is it appropriate to use BWA for the corrected PacBio long-reads?
Are some aligners more appropriate than others?