Question: Softwares for Bacterial/Viral Classification from RNAseq
0
gravatar for Ron
3.2 years ago by
Ron990
United States
Ron990 wrote:

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

sequencing rna-seq next-gen • 1.1k views
ADD COMMENTlink modified 3.0 years ago • written 3.2 years ago by Ron990

Have you explored making a custom database for Kraken?

ADD REPLYlink written 3.2 years ago by pld4.8k
0
gravatar for geek_y
3.2 years ago by
geek_y10k
Barcelona
geek_y10k wrote:

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.

ADD COMMENTlink written 3.2 years ago by geek_y10k
0
gravatar for Sej Modha
3.2 years ago by
Sej Modha4.6k
Glasgow, UK
Sej Modha4.6k wrote:

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.

ADD COMMENTlink written 3.2 years ago by Sej Modha4.6k
1

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

ADD REPLYlink written 3.2 years ago by genomax80k
0
gravatar for Ron
3.0 years ago by
Ron990
United States
Ron990 wrote:

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

ADD COMMENTlink written 3.0 years ago by Ron990
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