Introduce MoMIG: A Graph Genome Browser

[6br]

Hello, I would like to introduce that I have developed a beta version of a graph genome browser for human genomics. The name of the browser is "MoMIG" (Maple in Japanese): Modular Multi-scale Integrated Genome Graph Browser.

Features:

• genome graphs to visualize structural variants
• multi-scale view modules from whole-genome to a nucleotide
• modifiableness layout of modules on the dashboard

I have integrated VG and SequenceTubeMap into this browser to achieve these features. I really appreciate these tools and developers :)

In this CHM1 human haploid dataset, insertions, deletions, and inversions have been identified using long-reads. In this demo, all insertions and inversions are shown in the graph.

Using this demo, you can observe the distribution of variants with Circos Plot and select variants from feature table, and visualize the selected variant with SequenceTubeMap. You can also visualize the nested variants on the TubeMap.

I am very welcome any feedbacks/comments/suggestions!

Demo Page: http://chm1.momig.tokyo/

Manual: http://chm1.momig.tokyo/README.en.html

Short Demo Movie: https://youtu.be/Cv1OFREYtbU

[adamnovak]

This is pretty cool.

How do you change what part of the genome you are looking at in the tube map view? The demo seems stuck on chr5.

[6br]

There are some ways to select genomic regions.

1. Select variants from CIRCOS.
2. Select variants from variants table (click "⊕" button on each row).
3. Write down the genomic region on the input box of region buffer and click the double-circle button at the right-side of input box.

Could you look at these URLs?

• http://chm1.momig.tokyo/#annotations=true&layout=0&path=chr12%3A80842171-80861781&path=chr6%3A160956238-160956239&path=chr11%3A14863276-14863277&reference=hg19&uuid=
• http://chm1.momig.tokyo/#annotations=true&layout=0&path=chr6%3A160956238-160956239&path=chr12%3A80842171-80861781&path=chr11%3A14863276-14863277&reference=hg19&uuid=
• http://chm1.momig.tokyo/#annotations=true&layout=0&path=chr11%3A14863276-14863277&path=chr6%3A160956238-160956239&path=chr12%3A80842171-80861781&reference=hg19&uuid=

It requires a little bit longer time to acquire genome graphs from our internal backend server. Moreover, it returns no response if you select a long region(longer than 1Mb). So it may seem stuck. I will try to relaxes these performance issues.