Entering edit mode
4.7 years ago
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
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