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Pipeline for de novo analysis of bacteria genome

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
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written by agata88 agata88

1 answer

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.

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written by GenoMax GenoMax

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?

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written by agata88 agata88

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

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written by GenoMax GenoMax

Thank you very much. Best, Agata

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written by agata88 agata88

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