This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Bacterial Seq Alignment

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

alignment sequencing bacteria
• 1,305 views • link
written by ravihansa82 ravihansa82

1 answer

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.

• 0 views • link
written by volvox • volvox

Hi Volvox, Thank you for your suggestions.

• 0 views • link
written by ravihansa82 ravihansa82

Log in to answer this question.

More posts like this