Merge

Internal-only workflow: This page documents an operational sequence-processing automator. It must remain under docs/internal_only/ and must not be linked from the standard user index.

What does it do?

Use Merge to combine raw FASTQ data from multiple MiSeq runs of the same biological strain and generate a new merged assembly workflow record.

Merge is intended for authorized internal processing when repeated sequencing runs belong to the same isolate. The source runs must be verified as the same biological sample before submission.

How do I use it?

Subject

In the Subject field, enter:

Merge

Spelling matters, but matching is not case-sensitive.

Description

Leave the Description empty. Supply the complete request in one attached Excel workbook with the .xlsx extension.

Required attachment

The workbook must contain these exact headers:

Location — enter MER;
SEQID — new merged identifier in the form YYYY-MER-####;
OLNID — may be blank;
LabID — may be blank;
LabIDIsolate — may be blank;
OtherName — source SEQIDs separated by semicolons;
Genus — genus of the isolate; may be blank;
Species — may be blank;
Subspecies — may be blank;
Serotype — may be blank.

Example row concept:

Location: MER
SEQID: 2026-MER-0001
OtherName: 2026-SEQ-0001;2026-SEQ-0002

Use a genuine .xlsx workbook rather than a renamed CSV file.

Optional parameters

The supplied documentation does not identify optional Description parameters. Optional metadata columns may be left blank as noted above.

Example

See issue 14285 for an example Merge request and workbook.

Interpreting results

Merge returns the reports and assemblies normally produced by the WGS assembly workflow for the new merged record.

Verify that:

the new YYYY-MER-#### identifier is correct;
every source SEQID belongs to the same biological strain;
the resulting assembly and reports correspond to the merged input runs;
expected quality-control metrics improve or remain acceptable.

Merging additional sequencing data does not guarantee a better assembly if the runs are contaminated, mismatched, or poor quality.

How long does it take?

Runtime depends on sample count, read volume, and assembly workload. The supplied documentation estimates approximately 30 minutes per merged sample.

What can go wrong?

A source `SEQID` is unavailable

Symptom: The issue warns that one or more source runs cannot be found.

Likely cause: A source identifier in OtherName is incorrect or its FASTQ data are unavailable.

What to do: Verify each semicolon-separated source SEQID.

The workbook is missing or malformed

Symptom: The automator cannot parse the request.

Likely cause: No .xlsx file was attached, a required header is missing or misspelled, or the file is not a valid Excel workbook.

What to do: Use the required headers exactly and attach a valid .xlsx file.

The merged output identifier is invalid

Symptom: The workflow cannot create the new merged record.

Likely cause: Location is not MER, or SEQID does not follow the required YYYY-MER-#### format.

What to do: Correct both fields in the workbook.

Source runs belong to different isolates

Symptom: The merged assembly has poor quality, excessive fragmentation, conflicting taxonomic signals, or other unexpected results.

Likely cause: FASTQ data from different biological strains were combined.

What to do: Stop downstream use, verify sample identity, and repeat the workflow only with runs from the same strain.

Keep this page out of standard-access navigation and retrieval. Link it only from explicitly internal operational documentation.