how to characterize microbes in a fastq file of sewage microbiome

Question

[nazaninhoseinkhan]

Dear all,

I have received a fastq file of sewage microbiome.

I want to characterize the bacterial, fungal and viral sequences in this file.

Can I perform this analysis in Galaxy? I do not have any access to linux server and I have to do this using online servers.

And is there any microbial metagenome available for this task?

I will appreciate any advice in advance

Nazanin

Answer 1

[Joe]

What resolution do you want?

Take a look at Kraken. It will bin metagenomic reads in to genera. I think its available through Galaxy