The template can be downloaded directly from the website or from here (N.B You must be logged in first) This file is in CSV format. Please ensure that when editing in Excel you set all fields to be 'text format' not the default 'General format'. In particular pay attention to date fields that they remain as YYY-MM-DD.
An explanation for the fields for the sample can be found in the documentation section for Samples and for the library/sequencing fields are shown below
Required | Description | ​ |
Library Fields | ​ | ​ |
sequencing_org_received_date | no | Date sample received at sequencing organisation |
library_name | yes | A unique, memorable name for your library N.B multiple samples can have the same library but each library must have a unique name |
library_seq_kit | yes | e.g. LSK109 |
library_seq_protocol | yes | e.g. LIGATION |
library_layout_config | yes | One of SINGLE, PAIRED |
library_layout_insert_length | no | Nominal length of sequencing library insert (Integer). Illumina runs only. If left blank we will try and infer it from uploaded data. |
library_layout_read_length | no | Nominal length of sequencing library reads (Integer). Illumina runs only. If left blank we will try and infer it from uploaded data. |
library_selection | yes | One of RANDOM, PCR, RANDOM_PCR, OTHER |
library_source | yes | One of GENOMIC, TRANSCRIPTOMIC, METAGENOMIC, METATRANSCRIPTOMIC, VIRAL_RNA, OTHER |
library_strategy | yes | One of WGA, WGS, AMPLICON, OTHER |
barcode | no | N.B Not sample barcode but optional reference to barcode adaptor/number |
artic_primers | no | The version of primers used: 1 2 or 3 |
artic_protocol | ​ | The version of the lab protocol used |
Sequencing Run Fields | ​ | ​ |
run_name | yes | A unique name that corresponds to your run. You may use any string identifier, including a UUID N.B multiple samples can have the same run but each run must have a unique name |
instrument_make | yes | One of ILLUMINA, OXFORD_NANOPORE, PACIFIC_BIOSCIENCES |
instrument_model | yes | ​ |
start_time | no | Format: yyyy-mm-dd hh:mm |
end_time | no | Format: yyyy-mm-dd hh:mm |
flowcell_id | no | Flowcell serial number |
flowcell_type | no | Flowcell description |
bioinfo_pipe_name | no | The name of the bioinformatics pipeline used for downstream analysis of this run e.g ARTIC Pipeline (Nanopolish) |
bioinfo_pipe_version | no | The version number of the bioinformatics pipeline used for downstream analysis of this run |