I have some targeted genomic resequencing data I'm trying to assemble. The genomic region is highly variable, and I have reference sequences from 8 different haplotypes I can use. The 8 haplotypes differ considerably from one another. So far, I've only been able to assemble the data to one of the references at a time, but I would like to find a tool that would allow me to use all 8 concurrently and assembly contigs based on best match.
Does anyone know of an alignment tool that can use multiple reference sequences of the same genomic region simultaneously? Or, can anyone suggest a better approach to analyzing this data?
Does anyone know of an alignment tool that can use multiple reference sequences of the same genomic region simultaneously? Or, can anyone suggest a better approach to analyzing this data?
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