Reference Covering Issue Using Amplicon Reads

Question

[Sam]

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?

[Alex Paciorkowski]

Hi Sam, can you give us more information about what tool you are using for alignment?

Answer 1

[Ram]

If your have Sff format of your input file...try using Amplicon Variant Analyzer (AVA).