CEFAS23-139 RFQ for Illumina Sequencing of Metabarcoding Regions for GenePoolsII

Tender description

GenePools II is a citizen science project using eDNA to measure biodiversity in participants’ garden/urban ponds. The citizen scientists have been sent water sampling kits, which have been returned to Cefas for DNA extraction and quantification. Background: GenePools II is a citizen science project using eDNA to measure biodiversity in participants’ garden/urban ponds. The citizen scientists have been sent water sampling kits, which have been returned to Cefas for DNA extraction and quantification. This Request for Quotation is for amplicon sequencing (metabarcoding) of these samples using four primer sets, as described below. Sequencing to be carried out on Illumina MiSeq/NovaSeq platforms, as appropriate. Requirement: To aid with the above project, Cefas require Illumina sequencing of metabarcoding regions, as specified below; • DNA quantification for 250 DNA extracts from freshwater ponds • Preparation and sequencing of eukaryote 18S V4 amplicon metabarcoding libraries from each sample, to give a minimum of 20,000 reads per library (amplicon length c. 600bp) • Preparation and sequencing of invertebrate-targeted COI amplicon metabarcoding libraries to give a minimum of 10,000 reads per sample (amplicon length c. 200bp) • Preparation and sequencing of vertebrate-targeted 12S amplicon metabarcoding libraries to give a minimum of 5,000 reads per sample (amplicon length c. 200bp) • Preparation and sequencing of plant/green algal-targeted ITS2 amplicon metabarcoding libraries to give a minimum of 20,000 reads per sample (amplicon length c. 800bp) • Primer optimisation where necessary Cefas will make the final decision about which primers are used for generating the 18S, COI, ITS2, and 12S amplicons, after technical discussions with the successful Tenderer. Cefas require libraries to be barcoded with unique dual indexes and sequenced on an Illumina MiSeq or NovaSeq platform as appropriate with libraries from other projects (NovaSeq) or with PhiX control to maximise run diversity. Cefas require the data to be supplied in raw form with quality scores (fastq format, not demultiplexed), via FTP.