Best pipeline for annotation Helicobacter pylori with clc genome

[sinnamone]

Hi at all,

I'm new in this forum, i need your help. I have to to the annotation of three genomes of Helicobacter pylori (1,6MB) that i have sequenced with 454, one of them is the ref genome, in the first part of my work i'd like to do the annotation of all genes. The second part consist to analyze the genie expression. I'd like to use CLC genome workbench (6.5.1).
Somebody could help me to do a pipeline?

[GenoMax]

De novo assemblies in CLC: http://www.clcbio.com/files/tutorial..._and_BLAST.pdf

Re-sequencing based analysis in CLC: http://www.clcbio.com/files/tutorials/Resequencing.pdf

Either can be coupled to the Blast2Go in CLC (which requires a separate license I think) or you can use the web interface for Blast2Go: http://www.blast2go.com/b2ghome

That said if you do assemblies in CLC (and they are in a reasonably good state) then you could use NCBI's automated annotation pipeline for bacterial genomes: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/

[sinnamone]

Thank you GenoMax for reply.

I have read the tutorial for CLC in this days, we don't have a license for Blat2go. I have started my NGS analysis.

Import the file from 454 .fna in CLC, my input are three genomes, one (26695) is my reference genome, and the other two (SS1 and B128) are mutant genomes. Import the reads and I have selected the command "Map Reads to Reference"(http://www.clcbio.com/files/tutorials/Resequencing.pdf).

When CLC ask me Reference genome, i have selected Reference genome tracks that i have created following the tutorial. (http://www.clcbio.com/files/tutorial...ome_tracks.pdf)

Now if my steps are correct i would like to find a probabilistic variant and get a report with the most important of them.

Could somebody help me to improve my pipeline.