Christie - ARGOS Computation Statistics/Count

[cwoodside1278]

Provide numbers/ stats on the ARGOS computations number given what has been completed.

[cwoodside1278]

@lorikrammer here are the current stats:

Once I removed the duplicates (so only one assembly per organism is being run) we are left with 495.

Of the Organisms that I have computed from the NCBI Bioproject that are NOT in ARGOS: 34

Of the computations I have run that are re-runs from ARGOS: 25. There are two organisms I have yet to compute, because of genome issues.

So final stat is 59/495 as of Dec 9, 2024.

[cwoodside1278]

Will try to report new numbers once HIVE3 is fixed

[cwoodside1278]

Out of 3657 total SRA reads in FDA-ARGOS Bioproject 231221, 1843 are Illumina Platform @lorikrammer, because Raja asked for this number

[cwoodside1278]

as of today 68/495 assemblies have been run

[cwoodside1278]

Current count: 93 total organisms have been run so 93/495 (if counting one assembly per org).
91 bacteria and 2 Fungi
Assembley count: 109 bacterial assemblies and 2 fungi.

• There are some computations I have already run when redoing what was in ARGOS. Some have been accounted for already but not all. Just focusing on the NCBI bioproject orgs at the moment

[cwoodside1278]

I'll make it due the 18th for our next thesis meeting

[cwoodside1278]

As you can see by the subissue @lorikrammer @rajamazumder I have compared the 'Argos Rerun Table' to what I have currently run in the FDA-ARGOS BioProject. I wanted to see the final count of everything I have already run against what I have been running from the BioProject.

• Note: when I call soemthing an organism its at the end of the leaflet of that taxa tree. So Salmonella enterica and Salmonella enterica subsp. enterica serovar Typhimurium var. 5- are two separate organisms. Taht is because there are a bunch of assemblies under just Salmonella enterica and then Salmonella enterica subsp. enterica serovar Typhimurium var. 5- also has its own multiple assemblies

So here is the current count:

• Organism count: 134 Bacteria, 9 Virus, 4 Fungi
• Assembly count (includes multiple assemblies for each org): 204 Bacteria, 51 Virus, & 7 Fungi

[cwoodside1278]

As of Feb 25 2025, the current count is

• bacteria: organism - 161, assembly: 233
• virus: organism - 9, assembly: 51
• fungi: organism - 4, assembly: 7

174/495 as of Feb 23

291/1428 (with some being supressed)

[cwoodside1278]

@cwoodside1278 add the statistics/up the totals. Like what out of 495 and the total of assemblies.