Question: Annotate proteins from alignment (bacterial genome)
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gravatar for joshua.eunsong.craig
8 months ago by
joshua.eunsong.craig0 wrote:

Hello,

I have done full genome sequencing of strains of a bacteria, aligned them to a reference using BWA, and post-processed them for GATK with PICARD. However, I now want to check for presence/absence variation of individual genes in my alignments. I am wondering if there is a way to annotate my alignments, or, align to a reference alongside protein annotations (from NCBI Assembly, for example) to get a list of proteins.

Best

ADD COMMENTlink written 8 months ago by joshua.eunsong.craig0
1

See these posts below, most of them suggest Prokka for different sides of

bacterial annotation, but there are some additional suggestions as well.

Bacterial Annotation Pipeline

Bacterial genome annotation

A: Prokka Annotation for Bacterial Transcriptomes

ADD REPLYlink modified 8 months ago • written 8 months ago by natasha.sernova3.7k
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