Build A Spanning Tree From Several Strains

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2.7 years ago

davidmaimoun ▴ 50

Hi, I am new in the bioinformatics field. I need to check some close strains of listeria, make wgmlst and compare them in spanning tree. I don't know how to start, which pipeline/tools to use. I used SPAdes > chewBBAca > phyloviz, but the result is not good, I didn't get a spanning tree

Could you help me please?

Thank you

David

strains wgmlst compare tree spanning • 800 views

ADD COMMENT • link 2.7 years ago by davidmaimoun ▴ 50

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Hi David, please explain more about the data that you currently have.

ADD REPLY • link 2.7 years ago by Kevin Blighe 88k

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Hi, :)

I got fastq files from sratools, of 5 listeria strains, close to each others. I got contigs.fasta files after running SPAdes (de novo assembly) I used these files to run chewBBaca to create wgMLST profile (create schema > alleles calling > extraction for phyloviz). I got from ther extraction a tsv file I need to load with the phyloviz program (according to the docs) But I didn't get a minimum spanning tree

At work, they use Bionumerics to do that (to compare different isolates and determinate if there are risks of outbreak or not), and they want from me to find another way - linux tools way

Maybe my pipeline is wrong? You tell me..

Than you very much

ADD REPLY • link 2.7 years ago by davidmaimoun ▴ 50

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This is the file I need to run with phyloviz

ADD REPLY • link 2.7 years ago by davidmaimoun ▴ 50

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