Bacterial Seq Alignment

Question

[ravihansa82]

Hi Friends, 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 .. thank you

Answer 1

[volvox]

You can directly map your reads to the reference using bwa mem. I also suggest visually inspecting the bam file on IGV to check that the coverage is even, etc.

[ravihansa82]

Hi Volvox, Thank you for your suggestions.