Align whole closed and draft bacterial genomes

Question

[dago]

I would like to perform a whole genome alignment tree and a whole genome SNP calling.

I was thinking to use different tools (e.g. Gegenees, kSNP, Mauve).

My problem is that I have complete genomes and draft genomes. For the complete ones I have sometimes one or more plasmid.

What do you think is the best way of doing it, concatenating Chromosome and Plasmid and analyse them with the drafts or include in the analysis only the Chromosome and the drafts?

Answer 1

[Lee Katz]

You can check out the harvest package. Parsnp is great at aligning whole and draft genomes. If any genome is very fragmented, then it's probably a good idea to sort the contigs with something like abacus or contiguator before aligning them. Mauve, mummer, ksnp are all great tools and so most modern software choices should work for most things.

[dago]

thanks for your answer! So, you think I can analyse draft and complete together. For the complete one I would concatenate chromosome and plasmid and then analyse. What do you think?

[Lee Katz]

These programs will concatenate the sequences internally. Don't manually concatenate unless the program requires it.

[jeccy.J]

Hi Lee, i Did one parsnp analysis. Do you have any idea how to extract those gene and location which have high mutation rate??

Answer 2

[jeccy.J]

I am on same boat. For my data set my approach will be:

Do multiple alignment of all genome including plasmid and next find the conserved block among them and draw tree or else best approach may be core genome tree.