Explanation for the software "MUMmer"?

[prs321]

I am analyzing paired end reads of several strains of a bacteria along with the ancestor.

Questions that I am trying to answer:

1. Which genes exhibited change between the ancestor and the 3 treatment groups of bacteria (5 replicates)?

2. Are the genes that have changed between ancestor and treatment groups similiar among the treatment groups?

So far this is what I have done:

1. FastQC - report overrepresented sequences
2. cutadapt - cut adapter sequences
3. BWA - map to reference
4. Picard - Process SAM files (Clean, BAM, Sort, MarkDup, AddReadGroups, Merge)
5. Call SNPs with SAMtools

I left off at step 5 and found the number of SNPs between the 3 treatment groups. But at this point I'm not sure what to do in order to answer my 2 questions.

I was told to use MUMmer. I tried to read the manual, but I have no idea what's going on.

[aaronh]

MUMmer is a tool for whole genome alignments and it is not what you need. If you had two whole denovo assembled genomes then you would align them and look for differences. Since you already have the differences from you snp calling, time to move on to thinking about the genes. If you have an annotation, I would use snpEff or something like that. Also, are you sure you have found all the changes? SAMtools will not find things like large in/dels, CNV, or other structural changes.