Calculating haplotype and nucleotide diversity with deep amplicon sequencing data
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10 weeks ago
deorugz • 0


I want have deep amplicon sequencing data (illumina) where I have samples in row and haplotype (both sequences and names) in column and read counts.The dataframe is a CSV format and I have a separate file in fasta for the haplotypes. I read somewhere that someone has calculated nucleotide diversity and ASV heterozygosity (I suspect this is haplotype diversity) using the pegas software. I have managed to get nucleotide diversity data both in DNAsp and Arlequin. I was however curious how this was done in pegas. The thing that makes me think about it is especially how haplotype frequency is calculated in a samples( I think read counts are a poor representation of haplotype frequency, may of may not be true depending on the assumptions.

Can someone weigh in on this. It makes my head spin.

haplotype diversity Pegas Arlequin HTS_data • 237 views
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