Question: Pipeline for de novo analysis of bacteria genome
0
gravatar for agata88
8 days ago by
agata88720
Poland
agata88720 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 • 108 views
ADD COMMENTlink modified 8 days ago • written 8 days ago by agata88720
2
gravatar for genomax
8 days ago by
genomax54k
United States
genomax54k 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 8 days ago by genomax54k

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 7 days ago by agata88720
1

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

ADD REPLYlink written 7 days ago by genomax54k

Thank you very much. Best, Agata

ADD REPLYlink written 7 days ago by agata88720

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

ADD REPLYlink written 7 days ago by Kevin Blighe25k
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