Hello,

you might also consider to avoid an assembly and use virus databases to perform a classification based on sequence similarity. To get also a functional annotation of your sequences you can use tools that predict the function directly from the reads without any assembly. We have developed a tool named GAIA which can analyze metatranscriptomics, amplicon and WGS data. If you want to give it a look: https://metagenomics.sequentiabiotech.com/

Have a nice day

Riccardo Aiese Cigliano

Bioinformatician at www.sequentiabiotech.com

thanks for your answers...

Riccardo Aiese Cigliano

what would I do after detecting virus signal in a subset of reads?

still would be to do asseblemy, right?

thanks!

Hi Guillermo,

it finally depends on the goal of your project, if your aim is just to detect, classify and identify putative functions then you could avoid completely the assembly. If your goal is to obtain the actual sequence of the virus then you will have to make the assembly, still the mapping might be useful because you could extract all the reads mapping to the same genome and make an assembly of just those reads. By this way you could avoid the problem of creating chimeras or other artefacts.

Also the filtering of the contigs/scaffolds depends on your final goal and the kind of sensitivity or accuracy that you want to obtain. For instance if you are more interested in pulling out all the possible genes from your virus than you could use a very relaxed filter (for instance the double of the read size) whereas if you are more interested in an accurate and contiguous assembly you could use a more stringent filter.

I hope this helps,

kind regards

Riccardo

Bioinformatician @ www.sequentiabiotech.com