CoGDat Metadata
Regular Metadata
For the CoGDat data portal currently the following metadata are defined:
Lab-ENA-ID (optional)
The submitter ENA ID of the sample. If an ENA ID is specified here, CoGDat assumes that the submitter has already submitted the case to ENA and will not create a new submission to ENA for this case. If no ENA ID is specified here, the submitter guarantes that they will not create an ENA submission and agrees that CoGDat will submit the case to ENA.
SampleDate (optional)
The collection date of the sample.
The date has to be specified in the format YYYY-MM-DD. If the metadata is submitted in an Excel sheet, the corresponding cells should either be formatted as text adhering to the aforementioned format or they should be formatted as date values. In the latter case they will be automatically converted.
AGS-5 (optional)
The first five digits of the community identification number (AGS) of the domicile of the patient the sample was collected from. This corresponds to the resolution of “Landkreis” / “kreisfreie Stadt” or “Bezirk” in the case of a city with districts.
The value has to contain exactly five digits, otherwise it will fail validation. When you are submitting or preparing metadata using Microsoft Excel or another spreadsheet program, make sure that the AGS code is formatted as plain text and not as a numeric value, as otherwise ZIP codes beginning with ‘0’ will fail validation.
RawFQ1
The filename of the FASTQ raw file. If the data originates from paired-end sequencing and two FASTQ
files have been produced, then this refers to the filename of the R1 file.
This is a file field. A file with the corresponding name will have to be uploaded and linked to the metadata in a joint submission
RawFQ2 (optional)
The filename of the R2 file, given that the data originates from paired-end sequencing.
This is a file field. A file with the corresponding name will have to be uploaded and linked to the metadata in a joint submission
AssemblyFA
The filename of the FASTA file containing the virus genome assembly.
This is a file field. A file with the corresponding name will have to be uploaded and linked to the metadata in a joint submission
SeqPlatform
The used sequencing platform. The field is constraint to a controlled vocabulary, the allowed values and the corresponding sequencing platforms are listed below:
| Value | Platform |
|---|---|
| LS454 | 454 technology |
| ILLUMINA | Illumina |
| PACBIO_SMRT | PacificBiosciences |
| ION_TORRENT | Ion Torrent Personal Genome Machine (PGM) |
| CAPILLARY | Sequencers based on capillary electrophoresis technology manufactured by LifeTech (formerly Applied BioSciences) |
| OXFORD_NANOPORE | Oxford Nanopore platform type |
| BGISEQ | BGI Next Generation Sequencing Platform |
| DNBSEQ | MGI DNBSEQ Platform |
SeqInstrument (optional)
The user sequencing instrument. The permitted values are
454 GS
454 GS 20
454 GS FLX
454 GS FLX+
454 GS FLX Titanium
454 GS Junior
HiSeq X Five
HiSeq X Ten
Illumina Genome Analyzer
Illumina Genome Analyzer II
Illumina Genome Analyzer IIx
Illumina HiScanSQ
Illumina HiSeq 1000
Illumina HiSeq 1500
Illumina HiSeq 2000
Illumina HiSeq 2500
Illumina HiSeq 3000
Illumina HiSeq 4000
Illumina iSeq 100
Illumina MiSeq
Illumina MiniSeq
Illumina NovaSeq 6000
NextSeq 500
NextSeq 550
PacBio RS
PacBio RS II
Sequel
Ion Torrent PGM
Ion Torrent Proton
Ion Torrent S5
Ion Torrent S5 XL
AB 3730xL Genetic Analyzer
AB 3730 Genetic Analyzer
AB 3500xL Genetic Analyzer
AB 3500 Genetic Analyzer
AB 3130xL Genetic Analyzer
AB 3130 Genetic Analyzer
AB 310 Genetic Analyzer
MinION
GridION
PromethION
BGISEQ-500
DNBSEQ-T7
DNBSEQ-G400
DNBSEQ-G50
DNBSEQ-G400 FAST
AmpKit
The used amplification kit. The field is constraint to a controlled vocabulary, the allowed values and the corresponding amplification kits are listed below:
| Value | Kit |
|---|---|
| COVIDSeq | Illumina COVIDSeq Test |
| NEBNext | NEBNext® ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®) |
| Twist | Twist-SARS-CoV-2 Research Panel |
| QIASeq | Artic-Primer with QIASeq FX DNA Library Kit |
| ArticV1 | Artic v1 primers + Quick protocol |
| ArticV3 | Artic v3 primers + Quick protocol |
| covseq | DKFZ covseq protocol |
PCRCt (optional)
The integer part of the PCR Ct value.