Hi all,
we have data from 40 different amplicons of different sizes (400 - 4000 bp) that have various coverage levels sequenced in a plant, hence LAA struggles with this dataset (clustering approach not optimal and uneven coverage main issues). Ultimately, I'd like to have a set of haplotypes/genotypes (polyploid plant) per individual, where I can simply estimate allele frequencies in a population later and to report variants. We tried Freebayes as well, but it splits the full amplicons into linked chunks, while source data (amplicon length) is what we need.
Hence, does anybody know a good tool to cluster/align CCS reads into amplicon specific haplotypes/genotypes as alternative to LAA ?
thanks !
we have data from 40 different amplicons of different sizes (400 - 4000 bp) that have various coverage levels sequenced in a plant, hence LAA struggles with this dataset (clustering approach not optimal and uneven coverage main issues). Ultimately, I'd like to have a set of haplotypes/genotypes (polyploid plant) per individual, where I can simply estimate allele frequencies in a population later and to report variants. We tried Freebayes as well, but it splits the full amplicons into linked chunks, while source data (amplicon length) is what we need.
Hence, does anybody know a good tool to cluster/align CCS reads into amplicon specific haplotypes/genotypes as alternative to LAA ?
thanks !
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