Annotate proteins from alignment (bacterial genome)
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.
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joshua.eunsong.craig •
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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