Tools for viral metagenomics profiling and abundance estimation using BAM file

Question

[rice.researcher]

My aim is to perform taxonomic classification and transcript abundance estimation of viral communities from metagenomics sequenced reads. As the first step, I mapped all the reads to a reference which was built (bowtie2-built) based on refseq viral genomes. Currently, I have SAM and BAM files, and I am looking for tool(s) which can perform the profiling task.

I have came across viRome package , but would like to know whether more tools/methods are available.

Answer 1

[Sej Modha]

If you are looking for a k-mer based tool then checkout: DisCVR and if you are interested in building de novo assemblies then you can use: MetaViC You might find this paper useful: Bioinformatics tools for analysing viral genomic data

[rice.researcher]

Sorry,I forgot to mention that my samples are from specific environments (like saline condition and sea sediments) and not based on a host like human. I check both tools,

DisCVR: It is mentioned that currently, the pipeline is suitable for human viruses. So its not an option in my case.

So, I decided to work with MetaViC. But I have a confusion in the entry point to the pipeline. Currently, I have non-human and rRNA removed clean viral reads which are mapped to Refseq database. So could you suggest me how can I proceed having a BAM file?

[Sej Modha]

Please accept the answer if it resolves your original question.

[Sej Modha]

If you already have "clean" reads in a BAM file then it is best to convert the BAM to fastq and run the second component of the MetaViC pipeline that should assemble the reads into contigs and supercontigs and classify them.

[rice.researcher]

Ok I got it, thanks!!