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