We designed several probes to enrich the virus, such as hpv, ebv, hbv, from the cancer tissue DNA samples.
Is there any tool that can directly typing these virus from the raw fq data?
If your probes are specific you should be able to do that. There is a paper that has a pipeline to do this in RNAseq data.
The fastest way to type the viruses directly from the fastq data would be to use a kmer abundance tool such as kraken2.
This approach is fast as it performs neither alignment nor assembly. If you want to know the actual sequence of the virus(es) in the sample, then you'll need to do assembly.
kraken, or other metagenomic tools, apply kmer strategy to search the virus status from the fq data.
Can it do further step, such as determine the HPV alleles (hpv18)?
And I will carefully review the tool, any comments and suggestions will be appreciated.
Yes, kraken2 classifies according to where in the taxonomic tree it can place the reads. If that's just HPV, then it'll classify it with that taxId, if the sequence is unique enough that it can be classified as HPV 18, the it'll allocate as that taxId
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