Reference Covering Issue Using Amplicon Reads
I got HBV amplicon reads from a patient, and want to reconstruct HBV quasispecies using a reference and the amplicon reads. When I aligned them to a given reference(3320 bp long) I noticed that the reads are not covering the entire reference. the tool I am using can't handle gaps. In such case , what people do?
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Hi Sam, can you give us more information about what tool you are using for alignment?