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:1
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Epic Link:
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Sprint:Summer 1, Summer 2, Summer 3, Summer 4
Description
GOAL: To try a preliminary test run of spades on a Kelsey dataset.
This is a simple pilot run.
From this we can learn some nuances of spades and do a new ticket to do an official run.
Rob will get the URC folks to make a module of the latest SPADES release from earlier this week.
Why Spades?
Trinity creates hundreds of thousands of contigs and is a messy difficult tool.
https://academic.oup.com/gigascience/article/8/9/giz100/5559527
"This article is from 2019, so it may be a little dated. It compared several de novo transcriptome assemblers, such as Trinity and Bloom. Something cool is that it calculates the k-mer size based on read length and it has a lower duplication ratio when compared to trinity or bloom." Brandon
Trinity has a massive duplication problem it seems.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
I have submitted a help ticket to the URC to have them make Spades a module.
That should solve the issue in the easiest manner for all!
| Sprint | Summer 1 [ 195 ] | Summer 1, Summer 2 [ 195, 196 ] |
| Rank | Ranked higher |
SPAdes 4.0.0 is now installed and available for use on the HPC cluster.
2 Spades runs were completed successfully. Waiting on the other two. Collected numerical data is being collected in the two spreadsheets below, I will complete the sheets as soon as I have the outputs from Nag and Tam.
Output file results: https://docs.google.com/spreadsheets/d/1Jnxqw9v8HoOMqpJAu8kRFLAuIw0vuc2YIE7irzs7Tn8/edit?usp=sharing
| Sprint | Summer 1, Summer 2 [ 195, 196 ] | Summer 1, Summer 2, Summer 3 [ 195, 196, 197 ] |
| Rank | Ranked higher |
| Sprint | Summer 1, Summer 2, Summer 3 [ 195, 196, 197 ] | Summer 1, Summer 2, Summer 3, Summer 4 [ 195, 196, 197, 198 ] |
| Rank | Ranked higher |
Tam finally completed, and all contigs have been generated for each variety.
| 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 ] |
Installed Spades v4.0.0, it is located in /projects/tomato_genome/sw
I tried to run a test script, but Python on the cluster is version 3.6.8, and the new spades only work with Python versions 3.8 and up.