Variant Analysis of PacBio Reads

Question

[pthom010]

I have several multifasta files that contain PacBio reads of a gene of interest. I have one file of multifastas for several genotypes of a particular species. I would like to do a variant analysis on these reads but don't know where to start. Would it be possible to do the following:

1. Map these reads to my original gene of interest,
2. Then filter reads based on an identity score,
3. Then take my filtered reads and do a variant analysis calling out SNPs or other polymorphisms between genotypes?

A GUI would be nice, but I expect to do this in R so any R-programs would be greatly appreciated. Thanks.

[GenoMax]

multifasta files that contain PacBio reads

Do you know if these were generated by CCS or are they individual subreads converted to fasta format? If latter they may have a significant amount of error in them.

[pthom010]

Unfortunately I believe it was the latter. The reads were multiplexed with two other experiments (beyond my control) and I'm left with several multifastas containing as manny as 300 reads.