VICUNA analysis questions. Visualising variation?

[Gideon Mordecai]

Hi,

I have used VICUNA to assemble some Illumina reads of a diverse virus which exists as a quasispecies. I have run the VICUNA assembly and plan to use V-FAT to merge my contigs.

I have managed to run the VICUNA analysis programme, as I would like to see the variation that exists within the population. However I can’t seem to make sense of the output. Is there any further documentation available on how to analyse the VICUNA analysis output?

I have managed to create alignments of variation within the contigs. Is there a further bit of software that can analyse these data? Ideally I would like to generate heat maps of where the variation lies within the viral genome.

I was also wondering if it is possible to run the vicuna analysis programme on merged contigs created by V-FAT?

Thank you very much for your help and for creating these great bits of software specifically for highly diverse viral populations!

Gideon

[Xiao Yang]

Hi Gideon,

I answered your questions below.

On Thu, Apr 24, 2014 at 4:40 AM, Gideon Mordecai <gid...@gmail.com> wrote:

Hi,

I have used VICUNA to assemble some Illumina reads of a diverse virus which exists as a quasispecies. I have run the VICUNA assembly and plan to use V-FAT to merge my contigs.

I have managed to run the VICUNA analysis programme, as I would like to see the variation that exists within the population. However I can’t seem to make sense of the output. Is there any further documentation available on how to analyse the VICUNA analysis output?

The purpose of Vicuna Analysis that print out contig profile is for visualizing how the contig has been built from the reads. For instance, if you want to visualizing the env region of the HIV, you can specify specific range of coordinates so that read composition of that region can be printed out. 

However, this program is not meant for variant analysis. 

  

I have managed to create alignments of variation within the contigs. Is there a further bit of software that can analyse these data? Ideally I would like to generate heat maps of where the variation lies within the viral genome.

I was also wondering if it is possible to run the vicuna analysis programme on merged contigs created by V-FAT?

As I explained above, the short answer is no. If you want to do variant analysis,

you can use V-Phaser2 on our program webpage to identify possible variants. 

You could refer to that program for instructions. Once you identified the variants and their frequencies using V-Phaser2, you can easily convert them to heatmaps.  

Thank you very much for your help and for creating these great bits of software specifically for highly diverse viral populations!

Gideon

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- Xiao

[Gideon Mordecai]

Hi Xiao,

Thanks for your prompt reply. 

Just in case anybody searching this is interested, what I did in the end was:

Use VICUNA analysis to print out the alignment of the reads that make up the contig of interest.

Convert this into fasta format using a tab2fasta python script.

Opened the fasta alignment file in geneious which can then create a consensus sequence of all the reads using the degenerate nucleotide code.

I will also use V-Phaser to do further variant analysis though!

Thanks again for your help,

Gideon

[gludish]

Hi Gideon, 

I will be doing something very similar, but I want to clarify: does Vicuna not export a consensus sequence in fasta format? I'd be looking to import the consensus into Geneious also to do the variants analyses, but thought Vicuna would give me the consensus directly. 

Thanks for any help, 

David

[Gideon Mordecai]

Hi David, 

Yep vicuna outputs consensus contigs in fasta format which you can scaffold into full genomes if your assembly is good enough. Feel free to ask any more questions.

Cheers,

Gideon

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