I have sequenced the whole genome of few bacteria strains on Ion Proton platform and have to analyse the data now. I do not have access to super computer for analysis at the moment. Is there any website/online tool that I can upload the fastq raw file and it assemble the genome and to do annotation?
In your torrent server, it is very easy to install some of the plugins for basic analyses (or request the plugins be installed). The Variant Caller plugin will call variants against the reference genome; the Assembler plugin will execute MIRA assemblies of the genomes in a given run.
I don't believe that you can get annotation from unassembled fastq reads, but I could be mistaken. You need to take your assemblies, order the contigs/scaffolds against your reference genome, then upload the assembled, ordered contig/scaffold fasta files to RAST (rast.nmpdr.org/) to get annotations.
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