Forum:Estimating intra-strain variation from sequencing data

Question

[utsavnp]

I am trying to figure out the best way to estimate intra-strain variation using data obtained from sequencing double-stranded DNA virus. How should I go about this ? What are the best tools available for this purpose?

[h.mon]

What kind of data? Do you have a reference genome?

edit: probably "forum" is not a good tag for your question.

[utsavnp]

It is paired end 300 * 300 data from Illumina Miseq. Yes, I do have a reference/consensus genome.

[h.mon]

Did you try V-Phaser2 or QUASR? They seem to be the state of the art on virus variant inference.

Answer 1

[Steven Lakin]

In our most recent paper submission on RNA viruses, we ended up using GSNAP for alignment (although any short read aligner would probably work): http://research-pub.gene.com/gmap/ and V-Phaser2 for variant calling. We then used MrBayes for phylogeny: http://mrbayes.sourceforge.net/, with a few steps in-between these for quality control.

Honestly though, your best bet if you don't know where to start is to do a literature search for publications accepted within the last 1.5 years or so and just see what people are successfully using in your field of research.