how to characterize microbes in a fastq file of sewage microbiome

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

next-gen microbiome analysis

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updated 9.3 years ago by Joe

• written 9.3 years ago by nazaninhoseinkhan

1 answer

What resolution do you want?

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

• 0 views • link

written 9.3 years ago by Joe

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