Pipeline for de novo analysis of bacteria genome

Question

[agata88]

Hi all!

What methodology do you use for de novo analysis for bacteria genome? I don't have reference sequence of bacteria genome, and would like to annotate all found proteins, RNAs, etc. in GFF or GenBank format.

Thanks for any suggestions,

Agata

Answer 1

[GenoMax]

Prokka is generally the recommended software package for this purpose.

If you don't mind making the genome eventually public then you can take advantage of NCBI's Prokaryotic Genome Annotation service.

[agata88]

Thanks for suggestions. I will try that.

But before, I am going to assemble reads into contigs with Abyss. A a result I will have a lot of contigs being duplicated, what tool would you recommend for contig clustering? For rnaseq de novo I found Corset (https://github.com/Oshlack/Corset/wiki). Do you know something similar for genome de novo analysis?

[GenoMax]

SPAdes is probably the best assembler for bacterial genomes. CD-HIT can be used for clustering, if needed.

[agata88]

Thank you very much. Best, Agata

[Kevin Blighe]

Another option is Rockhopper, but it's not great for annotating.