Removal of host sequences without reference genome

Question

[emiliomastriani]

Dear all, Suppose to have a collection of viral reads from NGS (Illumina) technology in fastq format. After the usual pre-processing step (addressed by fastp), I need to remove the host sequences (contaminants) without having the reference genome (I cannot use bowtie2 and samtools for mapping, of course). I have ready some approaches, but I am still not sure. Please, can someone suggest an appropriate strategy/starting point/approach? Thanks for your support.

Answer 1

[Mensur Dlakic]

You would help everyone by providing more details: what is the host, how big a genome vs. the viral genome, what is it you are considering, etc.

I have answered this question in several different contexts, so I will just give you links. I think it is worth reading all the posts in those pages.

• How can I remove contaminants from an assembled genome?
• Removal of host reads from shotgun metagenomics data.
• How to assemble viral genomes when my data contains host DNA as well

[emiliomastriani]

Hello, The goal of my project is to identify the correct taxonomy of the viral reads I have. We always know the host of our sample even if the reference genome is not available, like bat, rodents, human, or mosquito.