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][1]. 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 ][2], but would like to know whether more tools/methods are available. 


  [1]: https://www.biostars.org/p/13646/
  [2]: http://www.ark-genomics.org/bioinformatics/virome
If you are looking for a k-mer based tool then checkout: [DisCVR][1] and if you are interested in building de novo assemblies then you can use: [MetaViC][2]
You might find this paper useful: [Bioinformatics tools for analysing viral genomic data][3] 


  [1]: http://bioinformatics.cvr.ac.uk/discvr.php
  [2]: https://github.com/sejmodha/MetaViC
  [3]: http://boutique.oie.int/extrait/20orton271285.pdf