What kind of dataset do you have? Is it for evaluating CRISPR edits, metagenomic data, or something else? Do you have a reference sequence? Are you wanting to incorporate this into a plugin (as this is the plugin development forum)?
Is there a way to have a list of haplotypes (and frequency) [identical sequences] extracted from an amplicon Illumina sequencing data?
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Sorry, think I am in a wrong forum.
I actually have Illumina sequences of a pooled barcoded amplicons.
I need to recover which haplotypes I find in each library (barcode).
What I did was import fastq data do geneious prime, merge the paired files and map them back to a reference sequence. I am doing that for each library.
Now I would like to have a list of filtered haplotypes and their frequency in each library