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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
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MLST output visualization #92

Open mabouelk opened 4 years ago

mabouelk commented 4 years ago

Hi, how can we make graphic representation of the mlst output. I tried to use geoburst but this one require the output to be: The dataset format needed is flat text file where each line should have 8 tab separated values.The first value is the Sequence Type number and the following 7 values are the allele numbers for each gene. Example from Campylobacter jejuni dataset: 9 1 6 22 24 12 7 1 45 4 7 10 4 1 7 1 11 48 7 10 4 1 7 1 433 2 59 4 38 17 12 35 21 2 1 1 3 2 1 5 14 9 2 55 62 4 5 6 15 6 4 13 2 2 1 5

Is there any way to make the output like this one. or do you recommend a tool/package to visualize the mlst output.

image

tseemann commented 4 years ago

If you use

mlst --legacy --scheme campylobacter *.fasta

it will give you what you need?

Try phyloviz? http://www.phyloviz.net/ Or Geoburst? http://www.phyloviz.net/goeburst/