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


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.


ADD COMMENTlink written 17 months ago by joshua.eunsong.craig0

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 17 months ago • written 17 months ago by natasha.sernova3.8k
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