I'm currently looking for recommendations on a method for haplotyping. The input is a .sam file with reads mapped to a (known) reference. The reads come from a species with 2 haplotypes (human), rather than reconstructing the genome I want to reconstruct its both haplotypes.
The reads are long (~10,000 bp) with high error rate and lots of indels (3-15%, nucleotides are errors, a majority are indels).
I've found one in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073643/ but do not seem to be publicly available for download. Primarily I have problems to find what methods right now are considered the best, as well as being easy to install and use.