Genetic mosaicism painting

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  • Chromosome Painting

    • Pre-loaded examples

      With your own data

      Input files

      Chromosomes size and labels



      or upload your own


      Colors (optional)

      Choose existing palette



      or enter your own color data

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Welcome to GeMo


Mosaic visualization shows colored blocs on the chromosomes:


Data curation displays the ancestral components along the chromosomes 
on an interactive graph to help the mosaïc construction:


		
	

Preloaded data from published studies or generated with VCFHunter or TraceAncestor.
		
	

Generate a visualization with your custom chromosomes data.
		
	

Chromosome data format, each column tab separated
chr, len, centromereInf (optional), centromereSup (optional), label (optional)
example :
chr	len	centromereInf	centromereSup	label
chr01	37945898			AB
chr02	34728925		11000000	AB
chr03	40528553	15000000		AB
chr04	44598304	13000000	22000000	AB
chr05	46248384	23000000	26000000	AB
chr06	42818424	23000000	27000000	AB
chr07	38870123	20000000	23000000	AB
chr08	50124231	21000000	25000000	AB
chr09	47435180	25000000	29000000	AB
chr10	39038070	12000000	16000000	AB
chr11	34441343	15000000	20000000	AB
		
	

Enter a block file to display the mosaïc visualization :

chr	haplotype	start	end	ancestral_group
01	0	1	29070452	g4
01	1	1	29070452	g4
02	0	1	29511734	g4
02	1	1	29511734	g4



Enter a file containing the ancestral components along the chromosomes to display an interactive graph 
and generate a new mosaïc visualisation :

chr	start	end	V	T	S
chr01	1145	189582	0.001671983513048138	0.014082301923852172	0.0016386866759508464
chr01	189593	356965	0.0012441961973068657	0.012867234592909085	0.0018101312755326665
chr01	356968	488069	0.0011179557674005532	0.010035172902205201	0.000759432489203596
chr01	488097	633373	0.002678217164025965	0.010470727908771585	0.003896031529700906



Generating datasets
In order to generate ready-to-use datasets, analyses can be conducted with the following software:

* VCFHunter
VCFHunter is a suite of python scripts enabling chromosome painting of indivisual based on the contribution 
of ancestral groups using VCF files.
Please look at the tutorial: 
https://github.com/SouthGreenPlatform/VcfHunter/blob/master/turorial_painting_GEMO_visualization.md

* TraceAncestor
TraceAncestor permits to estimate the allelic dosage of ancestral alleles in hybrid individuals and then 
to perform chromosom painting.
Please look at the tutorial: 
https://github.com/SouthGreenPlatform/TraceAncestor_gemo
		
	

group	name	hex
un	undef_group	#b4b4b4
g6	group6	#c00000
g5	group5	#9a029a
g3	group3	#1440cd
g2	group2	#ffc000
g1	group1	#000000
g4	group4	#00b009
g7	group7	#b4b4b4
g0	group0	#000000

		
	

bed file example :
chr01	5287838	5289224	gene	0	-
chr01	15485703	15486813	gene	0	+
chr01	15490016	15492587	gene	0	+
chr02	2276353	2277821	gene	0	+
chr02	15358393	15361764	gene	0	+
		
	

Jbrowse link example : 
https://banana-genome-hub.southgreen.fr/content/m-acuminata-dh-pahang-version-2/

GeMo will generate tooltips when hovering over each chromosomal block. 
A link is displayed to explore a chromosome block directly on jbrowse. 


The mosaic data are sent as tracks to be viewed in jbrowse.