Hello all,
I have done some pyrosequencing on HCV samples with the amplicon spanning the HVR1. I also have a sample that contains a clonal sequence as a control for sequencing/homopolymer error.
From my limited background in the area it appears that the analysis software provided by Roche has limited capabilities when it comes to processing virus sequences. In particular AVA views the mutations as random which, in the context of a quasispecies population with a hypervariable region, isn't the case. Consequently it is difficult to define a consensus sequence that will capture the optimum amount of information from the data file.
Do any users on this forum have experience of handling 454 sequence data from virus amplicons? I note a recent paper (http://www.biomedcentral.com/1471-2105/13/S10/S6/) where the group developed algorithms to assist in the calling of true variants and that it an improvement on SHORAH. As yet though I haven't been able to implement it myself.
I be interested to learn of more examples where groups have developed their own solutions to the problem.
I have done some pyrosequencing on HCV samples with the amplicon spanning the HVR1. I also have a sample that contains a clonal sequence as a control for sequencing/homopolymer error.
From my limited background in the area it appears that the analysis software provided by Roche has limited capabilities when it comes to processing virus sequences. In particular AVA views the mutations as random which, in the context of a quasispecies population with a hypervariable region, isn't the case. Consequently it is difficult to define a consensus sequence that will capture the optimum amount of information from the data file.
Do any users on this forum have experience of handling 454 sequence data from virus amplicons? I note a recent paper (http://www.biomedcentral.com/1471-2105/13/S10/S6/) where the group developed algorithms to assist in the calling of true variants and that it an improvement on SHORAH. As yet though I haven't been able to implement it myself.
I be interested to learn of more examples where groups have developed their own solutions to the problem.
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