Instructions to update submissions

Basic update procedure

When updating only the metadata of previously submitted samples, the following fields of the metadata file must be filled:

is_update = True (so we know to treat the submission as an update)
isolate_identifier / strain_name = xxxxxxx (so we can match the updated metadata with the existing sample)

Additionally, of course, any column you would like to update must be filled as well.

⚠️ Keep in mind any information you submit as update will overwrite existing information for that sample. Therefore it’s best practice to only fill columns you actually want to update.

Example use cases

Updating only some metadata

• Fields that must be filled:

  • is_update

  • isolate_identifier / strain_name

  • [columns of metadata to update]

• Fields that must remain empty:

  • raw_dataset_filename (forward)

  • raw_dataset_filename (reverse)

  • FASTA filename

Indeed if a filename is listed in the metadata, SPSP will search in the submitted files for this updated file. If there is no file it will trigger an on hold status and require manual intervention and clarification with the submitter.

Best practice is to only fill columns that you wish to update, to avoid accidentally overwriting previously submitted information

Updating raw files (FASTQ)

Two scenarios can happen: (i) an update of a raw dataset already submitted to SPSP (because of e.g. a sample mismatch) or (ii) the sending of an additional raw dataset to SPSP (from a different sequencing technology).

In the first scenario, SPSP will treat this new file and subsequently extracted data as the most up to date version of the data.

In the second scenario, SPSP detects that the raw data was generated with a different technology (e.g. the primary upload was of short-reads and the update contains long-reads (or vice-versa)) and therefore keeps both raw datasets associated to the isolate.

• Fields that must be filled:

  • is_update, isolate_identifier / strain_name

  • raw_dataset_filename

  • library_preparation_kit

  • sequencing_platform

  • [columns of metadata to update]

When a filename is listed in the metadata, SPSP will search in the submitted files for this updated file. Please be sure that you submit the updated file alongside the metadata so that there is no error.

Updating assemblies (FASTA)

In this case the new FASTA will overwrite the existing FASTA.

• Fields that must be filled:

  • is_update

  • isolate_identifier / strain_name

  • orig_fasta_filename

  • library_preparation_kit

  • sequencing_platform

  • assembly_method

  • assembly_type

  • [columns of metadata to update]