Generating consensus sequence from bam file re: Variant analysis


I have just aligned a paired-end FastQ (R1 & R2) files to a published viral genome using Bowtie2. The end goal is to extract the aligning reads from this sample and obtain a consensus sequence. Then I’d like to eventually compare this and a reference sequence (published) to compare the differences between the two (I basically want to see if there is any nucleotide variation between the two samples), to help with primer design.

So, I have never done this type of pipeline before and would just like some assistance on creating and obtaining a consensus sequence. I use and not coding.

From what I gather there’s two steps:

  1. Call variants
  2. Include the variants into the reference sequence


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Hello @peeham

Please see the Galaxy Tutorials here:

That post also has more troubleshooting help links included, if you run into problems with a particular tool. If you find a problem or have a question about a particular tutorial, each has a feedback form near the end. Those reach the GTN (tutorial authors). You can also reach them at their Gitter channel here for quick questions or requests: