Use Case 3-3

Workflow for Use Case 3-3's aim

In ths Use Case, we take the datasets from Matranga et al., relevant in the context of Lassa and Ebola outbreak and epidemic response, to demonstrate the versatility of Metavisitor as well as its ability to generate high throughput reconstruction of viral genomes.

---

Input data for Use Case 3-3

As for the previous Use Cases, the first step is to collect all input data in an history that we will name Input data for Use Case 3-3.

• Create a new history
• Rename this history Input data for Use Case 3-3
• Using the tool Extract reads in FASTA/Q format from NCBI SRA, we are going to upload 63 paired end datasets.

For Ebola virus samples:

• Select the upload File tool and click on the Paste/Fetch data button. Name the file "Ebola_accessions" and copy-paste the following text:

  SRR id
  SRR1613381
  SRR1613377
  SRR1613382
  SRR1613378
  SRR1613383
  SRR1613379
  SRR1613384
  SRR1613380

• Click the "Start" button.

• Use the Download and Extract Reads in FASTA/Q format from NCBI SRA tool. Set "List of SRA accession" in "select input type" and enter "Ebola_accessions" as input. Execute the tool.
• Select Concatenate multiple datasets tail-to-head. Change "What type of data do you wish to concatenate?" to "Paired collection", set the collection as input and "Concatenate pairs of datasets" in "What type of concatenation do you wish to perform?".

When you are finished, you'll have 8 datasets. Make sure to verify their datatype is fastqsanger or fastqsanger.gz, and create a dataset collection (as explained in the previous chapter) of these 8 datasets that you will name Ebola virus.

For Lassa virus samples:

• Upload, Download and Concatenate the Lassa virus datasets the same way as above, but this time name the file "Lassa_accessions" and copy-paste this text:

  SRR id
  SRR1595772
  SRR1595696
  SRR1595665
  SRR1595500
  SRR1594619
  SRR1595943
  SRR1595673
  SRR1595797
  SRR1595763
  SRR1595558
  SRR1594664
  SRR1595909
  SRR1594651
  SRR1595835
  SRR1594698
  SRR1613388
  SRR1613389
  SRR1613390
  SRR1613391
  SRR1613392
  SRR1613393
  SRR1613394
  SRR1613395
  SRR1613396
  SRR1613397
  SRR1613398
  SRR1613399
  SRR1595853
  SRR1606288
  SRR1613412
  SRR1613403
  SRR1606277
  SRR1613386
  SRR1613387
  SRR1606267
  SRR1614275
  SRR1610580
  SRR1595846
  SRR1594606
  SRR1606236
  SRR1594723
  SRR1594671
  SRR1613414
  SRR1613400
  SRR1613401
  SRR1613404
  SRR1613402
  SRR1613405
  SRR1613407
  SRR1613408
  SRR1613409
  SRR1613410
  SRR1613406
  SRR1613411
  SRR1613413

When you are finished you'll have 55 datasets. Make sure their datatype is fastqsanger or fastqsanger.gz, and create a dataset collection (as explained in the previous chapter) of these 55 datasets that you will name Lassa virus.

• Copy the nucleotide vir2 blast database from the References history to the current history Input data for Use Case 3-3.

History for Use Case 3-3 / Ebola virus

1. Stay in the history Input data for Use Case 3-3
2. Pick the workflow Metavisitor: Workflow for Use Case 3-3 in the workflows menu, and select the run option.
3. Before Step 1, you have to specify some parameters at run time. For Ebola virus, the field reference_virus has to be filled with NC_002549.1 (as a guide for reconstruction of the Ebola virus genome) and the field target_virus has to be filled with Ebola.
4. For Step 1, select Ebola virus.
5. For Step 2, select the nucleotide vir2 blast database (this should also be already selected)
6. As usual, check the box Send results to a new history, edit the name of the new history to Use Case 3-3 Ebola virus, and Execute the workflow ! Note, that for complex workflows with dataset collections in input, the actual warning that the workflow is started make take time to show up; you can even have a "504 Gateway Time-out" warning. This is not a serious issue: just go in your User -> Saved history menu, you will see your Use Case 3-3 Ebola virus history running and you will be able to access it.

The workflow for Use Case 3-3 may take a long time. Be patient.

History for Use Case 3-3 / Lassa virus, segment L

1. Stay in the history Input data for Use Case 3-3
2. Pick the workflow Metavisitor: Workflow for Use Case 3-3 in the workflows menu, and select the run option.
3. Before Step 1, you have to specify some parameters at run time. For Lassa virus, the field reference_virus has to be filled with NC_004297.1 (as a guide for reconstruction of the segment L of the Lassa virus genome) and the field target_virus has to be filled with Lassa.
4. For Step 1, select Lassa virus.
5. For Step 2, select the nucleotide vir2 blast database (this should also be already selected)
6. As usual, check the box Send results to a new history, edit the name of the new history to Use Case 3-3 Lassa virus segment L, and Execute the workflow ! Note, that for complex workflows with dataset collections in input, the actual warning that the workflow is started make take time to show up; you can even have a "504 Gateway Time-out" warning. This is not a serious issue: just go in your User -> Saved history menu, you will see your Use Case 3-3 Lassa virus segment L history running and you will be able to access it.

The workflow for Use Case 3-3 may take a long time. Be patient.

History for Use Case 3-3 / Lassa virus, segment S

1. Stay in the history Input data for Use Case 3-3
2. Pick the workflow Metavisitor: Workflow for Use Case 3-3 in the workflows menu, and select the run option.
3. Before Step 1, you have to specify some parameters at run time. For Lassa virus, the field reference_virus has to be filled with NC_004296.1 (as a guide for reconstruction of the segment S of the Lassa virus genome) and the field target_virus has to be filled with Lassa.
4. For Step 1, select Lassa virus (this should be already selected).
5. For Step 2, select the nucleotide vir2 blast database (this should also be already selected)
6. As usual, check the box Send results to a new history, edit the name of the new history to Use Case 3-3 Lassa virus segment S, and Execute the workflow ! Note, that for complex workflows with dataset collections in input, the actual warning that the workflow is started make take time to show up; you can even have a "504 Gateway Time-out" warning. This is not a serious issue: just go in your User -> Saved history menu, you will see your Use Case 3-3 Lassa virus segment S history running and you will be able to access it.

The workflow for Use Case 3-3 may take a long time. Be patient.