Viral genome assembly from RNA-seq data

[mcastro]

Hi,

I'm performing a RNA-seq analysis from a virus infected plant. After mapping the Illumina Hiseq paired reads against the plant genome, I used the unmapped reads to blast the virus genome available. Once I separated virus reads from other unmapped reads I would like to assembly the virus genome. Which is the best way to do it? I used before velvet and trinity for eukaryote transcriptome assemblies but I'm not sure if I can use the same software or approach for virus.

I would appreciate someone could guide me.

Thanks a lot

[dramit1623]

Dear,

generally i used bowtie first then samtools to generate mapped reads and then use Macvector software to assemble the genome.

thanks.

[blancha]

This is a very naive question, but how can you be sure that the unmapped reads belong to a virus?

Isn't it just as likely that they belong to unmapped regions of the plant transcriptome, sequencing errors, ...?