Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Fall 4, Fall 5
Description
Goal: to explore what it will take to do graph based alignments to multiple tomato sequence genomes.
This is based on Liz's comments last week.
This will also be valuable preliminary research into going after a future tomato pan genome on a larger scale.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Description |
Goal: to explore what it will take to do graph based alignments to multiple tomato sequence genomes. This is based on Liz's comments last week. This will also be valuable preliminary research into going after a future tomato pan genome on a larger scale. |
Goal: to explore what it will take to do graph based alignments to multiple tomato sequence genomes.
This is based on Liz's comments last week. This will also be valuable preliminary research into going after a future tomato pan genome on a larger scale. |
| Sprint | Fall 4 [ 205 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
An excellent overview of pan genome tools used in mapping and graph generation:
https://www.youtube.com/watch?v=_gocn57ZNck
VG tool suite (cactus, etc., ) seems to have many great features.
| Sprint | Fall 4 [ 205 ] | Fall 4, Fall 5 [ 205, 206 ] |
| Rank | Ranked higher |
Minigraph-cactus seems like a cool tool that we could investigate and possibly apply to our data. It perform iterative genome alignment and constructs a graph directly from assemblies. Github: https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md
Another tool I am going to look into is PanGenome Graph Builder (PGGB), this one claims to solve the problems surrounding whole genome alignment. Github: https://github.com/pangenome/pggb
These are the two tools discussed in the above you tube video.
I was thinking of installing a version of Minigraph- Cactus onto the cluster to test it out, but it needs python version 3.8 at the minimum and we only have version 3.6.8.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Reached out to James to get his opinions on this topic and the tomato pan genome in general.