Bacterial Seq Alignment
I have illumina paired end seq reads for my bacterial species. Now I need to align it to a reference genome. What are the best methods for sequence read alignment? Should I first do de novo assembly ( I am planning to use SPAdes or velvet tools) then align the assembled data to a reference genome or is it good enough to use the BWA-mem algorithm and align the reads directly with the reference genome?
I highly appreciate your ideas ..
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