Estimating haplotypes from sequencing reads

Question

[Arline]

Hello,

Do you know how to estimate number of haplotypes from sequencing reads and what tools to use in linux?

Thanks in advance for your help

Arline

[Pierre Lindenbaum]

how is it different from your previous question ? How to count number of haplotypes and haplotype frequency from phased vcf files?

[Arline]

In my previous question, I tried to used vcf phased files with snps and indels while for my last question I want to estimate directly from sequencing reads

[Michael]

Do you have long reads and short-reads? Then this could be done with nphase2 or whatshap. Long read assemblers can also generate alternative haplotypes during assembly. If you only have short reads I would say that the resulting haplotype clusters won't be very useful.

[Arline]

In fact, we have sequenced a pool of microfilariae (juvenile larvae) and we want to estimate the number of parents that generated the juvenile larvae by trying to estimate the number of haplotypes seen in the microfilariae sequences.

We did a sequencing with illumina and the reads have a length of 50-150 bp