Samples and Library/Run Metadata

1. To bulk upload multiple samples and their associated sequencing information, download the template and fill in the fields.
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

Samples Metadata Only

Library/Run Metadata Only

Last updated 3 months ago

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