How to use genetic map (markers.csv) file to scafold a haplotype phased assembly from contig level to pseudochromosome level.

[ap1438]

have a Genetic map (18000_markers.csv) in ABH format and i want to use this genetic map to scaffold a contig level assembly(I have 2 haplotype phased genome assembly).

I figured out that this can be achived using ALLMAPS .But the input file in all maps looks different than what i posses and i am new to using genetic map and donot know how to convert the file that i have to be used to scafold the haplotype phased genomes.

I have below an example of the file i have and i donot know how to attach the .csv file for convenience.

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id	chr1_153600	chr1_202763	chr1_211008	chr1_211360	chr1_237927	chr1_294054	chr1_315629	chr1_221454	chr1_237913	chr1_214484	chr1_348473	chr1_317931	chr1_393124	chr1_410996	chr1_441148	chr1_444094	chr1_509974	chr1_515004	chr1_515498	chr1_516081	chr1_520420	chr1_520449	chr1_522093	chr1_522229	chr1_522520	chr1_522530	chr1_533422	chr1_537039	chr1_537048	chr1_537275	chr1_552942
	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1	L.1
	0	0.000001	0.000002	0.000003	0.000004	0.000005	0.000006	0.000007	0.000008	0.000009	0.00001	0.000011	0.000012	0.000013	0.000014	0.000015	0.000016	0.000017	0.000018	0.000019	0.00002	0.000021	0.000022	0.000023	0.000024	0.000025	0.000026	0.000027	0.000028	0.000029	0.00003
1_a1	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B
10_a10	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A
100_a100	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
101_a101	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
102_a102	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A
103_a103	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B
104_a104	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
105_a105	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A
106_a106	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
107_a107	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
108_a108	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
109_a109	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B
11_a11	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
110_a110	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
111_a111	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A
112_a112	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
113_a113	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A
114_a114	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A
115_a115	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
116_a116	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B
117_a117	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
119_a119	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H	H
12_a12	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B

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Please let me know how can i scaffold the genome. Thanks in advance for your valuable time.

[tanghaibao]

@ap1438

I think you may need to construct the genetic map first. The format you have here is very similar to MSTMap input. http://alumni.cs.ucr.edu/~yonghui/mstmap.html

Once you have computed the genetic distance for all markers, then you can follow the steps in https://github.com/tanghaibao/jcvi/wiki/ALLMAPS#step-1-prepare-input-data to use ALLMAPS.

[ap1438]

I got this result. I am not familiar with theses type of plots and what to interpret from this.

Does this just mean that, for Chr 3, have linkage to two linkage groups (that means markers from linkage group 2 i.e corresponding to chr. 2 , also map to chr.3 )Or is something more concerning going on?
-I can interpreter that there are disagreements between the position of the marker in genetic map and physical map.
-What does the grey colour signifies in the bar of ChrL.3(28mb). What does vertical lines on the graph means.

• If there are disagreements should I question the quality of the linkage map and/or genome assembly?
• -Can i locate and extract the exact region of disagreement from any output file produced by allmaps?
• Should i check the assembly by aligning the contigs back to the assembly and check the regions of disagreement for validation.
  Any help would be much appreciated.
  chrL.3.pdf

This one seems even more chaotic.

chrL.8.pdf

Thanks for your valuable time.

[tanghaibao]

@ap1438

The assembly looks reasonable to me and the matching to multiple linkage groups does not seem too concerning.

The grey colors are showing contigs that get assembled (so grey, white, grey, white ... alternating colors so that you can see the boundaries of contigs). In your case, there are just 2 contigs. This is the best arrangement between the two contigs that agree with the linkage map.

If you look at the matches to other linkage group (X-L.2), they are really minor and appears concentrated on a few places. You can increase --links to remove those minor matches.

Same story on the chr8, it doesn't seem bad at all.

[ap1438]

Thank You

[ap1438]

Refering to - You can increase --links to remove those minor matches.

How does this --links option work and what value should be reasonable to increase. I increased it to 20 and it did remove some minor matches but not in all the chromosomes. So, i was curious to know what exactly this option does and what should be an optimal value.

Can you please explain this.