Merge

What does it do?

Merge will take data from multiple MiSeq runs of the same strain and combine the FASTQ files in order to produce a better assembly.

How do I use it?

Subject

In the Subject field, put Merge. Spelling counts, but case sensitivity doesn't.

Description

No text necessary in the description. You will, however, need to attach an excel file (.xlsx extension) with the following headers:

  • Location: Should be 'MER'
  • SEQID: Put the name of the merged SEQID (YYYY-MER-####)
  • OLNID: Can be blank
  • LabID: Can be blank
  • LabIDIsolate: Can be blank
  • OtherName: The SeqIDs you want to merge, separated by semi-colons.
  • Genus: Genus of the isolate. Can be left blank.
  • Species: Can be blank
  • Subspecies: Can be blank
  • Serotype: Can be blank

An example file can be found with the example issue below.

Example

For an example Merge, see issue 14285.

Interpreting Results

You'll get back the reports and assemblies, as you would for a WGS Assembly issue.

How long does it take?

Merge will take quite a while, depending on how many samples you have. Probably roughly half an hour per sample.

What can go wrong?

1) Requested SEQIDs are not available. If we can't find some of the SEQIDs that you request, you will get a warning message informing you of it.