Build Phylogenetic Tree from SNPs

Question

[davidmaimoun]

Hello, I am new (very new!) in the field of bioinformatics. I try to learn on my own, but it is sometimes difficult. My boss gave me a project: take 5 strains of Listeria, do all the identification work to end up by building a tree representing the genetic distance between them (based on nucleotide sequences). From fastq I did trimming > assembly de novo > annotation > scaffolding And now...I don't know! I guess I have to do an msa, but I don't know what to put in input...and then how the result can lead me to the requested tree It would be wonderful if you can offer me your help!

David

[guillaume.rbt]

Could you explain why did you do an assembly de novo?

You could use a reference genome to align your reads, do a variant calling, then use the detected SNPs of housekeeping genes to do your phylogenetic trees.

Answer 1

[liorglic]

No need to assemble and annotate your data. Take your fastq files and map them to the reference Listeria genome (e.g. using BWA), then perform a variant calling procedure (using bcftools mpileup or GATK). Once you have your SNP calling in VCF format, you can use the SNPhylo pipeline or IQTREE to reconstruct the phylogeny from SNPs. This is a very general outline and you may want to tweak each step to improve your results. I suggest that you start by finding some papers from recent years that did something similar, and follow their procedure. Good luck!

Answer 2

[Matthias Zepper]

I think, PhyloPhlAn can be used for what you are aiming to do...see this example plot.

Answer 3

[davidmaimoun]

Thank you so much for your help guys,

I very new in the field and I got very confuse with all the tools and pipeline, when to do SNP calling, and when to do allele calling (but I need to learn how to make both of them). I got job in the ministry of health. Basically, I need to check if the isolates we got from people are the same strain and if there is a risk of epidemia.

Again thank you very much, your answers are very useful!