Mazumder - Select ngs data for Candida Auris, provide justification, and add data to ngsQC_HIVE

[steph-sing]

Data Selected via this Protocol and justification: Fungi_Data_selection_protocol_SS1

1. Candida auris genome assembly selected: https://www.ncbi.nlm.nih.gov/assembly/GCA_002759435.2/

2. This NGS data is associated with the selected genome assembly, which is associated with the last outbreak between 2015-2018. Data was collected by the CDC and others:

   • BioSample: SAMN05379624
   • 64 SRA Experiments: SRA-PRJNA328792
   • BioProject (Data from two different papers): PRJNA328792
   • Use the attached tracking sheet to identify which SRRs to QC: Candida_auris_PRJNA328792.csv

3. NGS Data associated with the most recent outbreak, also collected by the CDC, is in the following BioProject and has the following data:

   • Candida auris in the United States
   • BioProject: PRJNA940794
   • 117 SRA Experiments: SRA-PRJNA940794
   • Use the attached tracking sheet to identify which SRRs to QC: Candida_auris_PRJNA940794.csv

@JingyueWu

• [x] Please QC all ngs data, add to the ngsQC sheet, and reassign for Joe or I to review.
• [x] please add all new entries into the [QC Organism Tracking] (https://docs.google.com/spreadsheets/d/1Nf9Eey2ruwKRkoSMoNhGCAYmFAw2Wb73TzA3sYA3va0/edit?usp=sharing) in the 'Orgs_in_NCBI_QC_Tracker' Tab

[steph-sing]

@JingyueWu prioritize #3 in the list above

[steph-sing]

here is another reference genome cited by the group and under the same BioProject: https://www.ncbi.nlm.nih.gov/assembly/GCF_003013715.1/ @penningtonea can you please look into the this more?

[JingyueWu]

@steph-sing Status update (as of 5:30 pm April 11):

As instructed to prioritize 3), I have added the 117 SRAs into the QC Organism Tracking. Since there are 117 total, which is a lot, I highlighted 10 SRAs in the same color for now. That way, it is easier for me to keep track of them as I run ngsQC on them.

This afternoon, I finished running 20 SRAs (highlighted in green and pink on QC Organism Tracking). Their corresponding ngsQC metrics were entered on ngsQC_HIVE (starting from row 2198) from V1.3 folder.

I will continue this tomorrow. I foresee no blockers, but the parts that took the longest time were 1) to get those SRRs into HIVE, and 2) each time after ngsDataGrabber script was run, HIVE automatically logs me out.

[JingyueWu]

Status update: all 117 SRR's in 3) have been ngsQC'd and their metrics were recorded here, starting from row 2198.

In addition, the new entries were recorded on QC Organism Tracking (second tab)

• [x] @Jgergely11 Please review the above.

[Jgergely11]

@JingyueWu Please resolve the issues outlined below

• [x] Fill out "lineage" column
• [x] Fill out "taxid" column
• [x] Fix formatting in "analysis_platform" column
• [x] Fill out "analysis_platform_object_id"
• [x] Fill out "strain" column
• [x] Fix formatting in "bioproject" column
• [x] Fix formatting in "ngs_gc_content" column
• [x] Fill out "instrument" column
• [x] Fix formatting in all columns with pipes (there needs to be a space after each | ). You can isolate your data and do a find and replace search. Replace "|" with "| "

[penningtonea]

here is another reference genome cited by the group and under the same BioProject: https://www.ncbi.nlm.nih.gov/assembly/GCF_003013715.1/ @penningtonea can you please look into the this more?

Would you like me to QC this assembly and compare to GCA_002759435.2?

[JingyueWu]

@Jgergely11 Fixed. Please review.