Softwares for Bacterial/Viral Classification from RNAseq

Question

[Ron]

Hi all,

I am working with bacterial viral classification of RNAseq reads and have tried Kraken https://ccb.jhu.edu/software/kraken/ But its not giving good results.Its missing the viruses that are known thats present in the samples and have been detected by Fusion catcher as well.(Although fusion catcher is for fusion detection but it also gives viral reads information)

I have tried installing SURPI , but it took a lot of time to install it and eventually gave up on it. http://chiulab.ucsf.edu/surpi/

Any other software suggestions for this purpose?

Thanks, Ron

[pld]

Have you explored making a custom database for Kraken?

Answer 1

[GouthamAtla]

I am not sure if there are better pipelines than SURPI. I had written a post long back with installation and running issues of SURPI Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.

Check if it helps.

Answer 2

[Sej Modha]

If you are interested in read-based analysis then it's worth trying DIAMOND which is a much faster alternative to BLASTX and BLASTP. It is straightforward to install and run.

[GenoMax]

While I like DIAMOND it is fair to mention that it will require significant resources, especially if you are going to blastx against nr.

Answer 3

[Ron]

VirusFinder: Software for Efficient and Accurate Detection of Viruses and Their Integration Sites in Host Genomes through Next Generation Sequencing Data

I came across this software and its easy to install compared to the others,and it gives good results. e.g. I had some samples positive for viruses and it was able to detect those in them.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064465