Question: Pipeline for de novo analysis of bacteria genome
0
gravatar for agata88
10 weeks ago by
agata88740
Poland
agata88740 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 • 214 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by agata88740
2
gravatar for genomax
10 weeks ago by
genomax57k
United States
genomax57k 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 10 weeks ago by genomax57k

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 9 weeks ago by agata88740
1

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

ADD REPLYlink written 9 weeks ago by genomax57k

Thank you very much. Best, Agata

ADD REPLYlink written 9 weeks ago by agata88740

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

ADD REPLYlink written 9 weeks ago by Kevin Blighe30k
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