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.