Question: Tools for viral metagenomics profiling and abundance estimation using BAM file
1
gravatar for rice.researcher
14 days ago by
Korea, Republic Of
rice.researcher80 wrote:

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.

ADD COMMENTlink modified 14 days ago • written 14 days ago by rice.researcher80
2
gravatar for Sej Modha
14 days ago by
Sej Modha2.2k
Glasgow, UK
Sej Modha2.2k wrote:

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

ADD COMMENTlink modified 14 days ago • written 14 days ago by Sej Modha2.2k

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?

ADD REPLYlink modified 11 days ago • written 14 days ago by rice.researcher80

Please accept the answer if it resolves your original question.

ADD REPLYlink written 11 days ago by Sej Modha2.2k

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.

ADD REPLYlink written 10 days ago by Sej Modha2.2k

Ok I got it, thanks!!

ADD REPLYlink written 10 days ago by rice.researcher80
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