Question: Pipeline for de novo analysis of bacteria genome
0
gravatar for agata88
4 months ago by
agata88760
Poland
agata88760 wrote:

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

bacteria genome • 277 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by agata88760
2
gravatar for genomax
4 months ago by
genomax59k
United States
genomax59k wrote:

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.

ADD COMMENTlink written 4 months ago by genomax59k

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?

ADD REPLYlink written 4 months ago by agata88760
1

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

ADD REPLYlink written 4 months ago by genomax59k

Thank you very much. Best, Agata

ADD REPLYlink written 4 months ago by agata88760

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

ADD REPLYlink written 4 months ago by Kevin Blighe33k
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