Possible to leverage this tool for classifying short reads?

jiarong / VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data

GNU General Public License v2.0

225 stars 31 forks source link

Possible to leverage this tool for classifying short reads? #85

Closed UCRajkumar closed 3 years ago

UCRajkumar commented 3 years ago

I realize this tool is used to classify viral genomes. However, is it possible to leverage this tool to classify short reads (150 bp) as viral/non-viral?

jiarong commented 3 years ago

Hi, VirSorter2 is not suitable for short reads. Kmer-based methods such as DeepVirFinder have better performance on shorter sequences (<3kb), but still does NOT work well with short reads..