6640--Oxford Nanopore GridION and P2 Solo

A. GENERAL INFORMATION

Title of Project: Purchase of the Oxford Nanopore GridION and PromethION P2 Solo Sequencing Devices

Scope of Work: The Research Department located at the Central Texas Veterans Health Care System (CTVHCS), 1901 S. 1st Street, Temple, Texas is requesting to purchase a new contract for the Oxford Nanopore GridION and PromethION 2 Solo.

Background: Dr. Jinadatha s Infectious Disease Research group requires a new contract for the Oxford Nanopore GridION and PromethION 2 Solo sequencing systems. These high-quality sequencing systems are critical pieces of equipment that are required for completion of VA funded research projects at our facility. The instruments need to be able to perform genome sequencing for various microbial samples. The instruments must enable long read sequencing, which is different to most other sequencing systems, as well as accommodate for protocol changes necessary for the lab s unique sample set. Whole genome sequencing is a useful tool in many applications such as microbial identification, antibiotic resistance detection, infection control, epidemiological investigation, and metagenomics. Long read sequencing is necessary to the work completed in this lab due to several aspects including detection of complex structural variants, repetitive regions, and plasmids; metagenomic identification of closely related species; simplifying library preparation for sequencing and assembly after reads. The simplified library preparation process means that significant research time and funding is saved by using a long-read sequencer. Additionally, this lab already has a similar piece of equipment from the same company, so researchers are familiar with the technology.

DESCRIPTION of EQUIPMENT: This requested pieces of equipment must have all of the following attributes and capabilities:

Sequencing Device 1: GridION

Instrument should allow for flexible sequencing of whole genomes, targeted regions, and full-length RNA transcripts

System reads the length of DNA or RNA presented from short to ultra-long (longest >4Mb)

Integrated real-time data processing

Long-read, real-time nanopore sequencing

Five flow cells

Ability to control each flow cell individually- run as many or as few as needed at the same time, or add more while the others are running

250 Gb yield, up to 50 Gb per MinION Flow Cell / 2.8 Gb per Flongle Flow Cell

Ethernet, USB2, USB3, USB-C ports

Storage: 4TB SSD

Memory: 64 GB RAM

Sliding lid

Compact benchtop device weighing no more than 11kg, size: W 37cm, H 22cm, D 36.5cm

Remote installation support call

Includes one-year software license and device warranty

All service repairs will be called in by selected research technicians designated by COR

Sequencing Device 2: PromethION P2 Solo

Ability to connect to GridION instrument

Two high-yield flow cells delivering up to 580 Gb of data

Ability to run flow cells individually or together

Generate 100-200 Gb native gDNA reads (read N50-25 kb)

>100 million cDNA reads for isoform-level analysis

Multiplexed sequencing of up to 96 samples with PCR or PCR-free barcoding

50-100 Gb ultra-long native DNA reads (>50kb read N50)

>200 Gb on metagenomic samples (read N50 ~ 10 kb)

Uses same chemistry and kits as GridION

Includes one-year software license and device warranty

All service repairs will be called in by selected research technicians designated by COR

Consumables

Rapid Barcoding Kit 96 V14

Ligation Sequencing Kit V14

Native Barcoding Kit 96 V14

Flow Cell Wash Kit

Flow Cell Priming Kit

Ultra-Long DNA Sequencing Kit

SHIPPING: Shipping needs to be performed by personnel trained to safely transport sensitive equipment.

Training: Advanced training package for GridION should include the following:

On-site training by a technical specialist

2.5 day duration

Experimental design and quality control

Library preparation for 1x control and up to 4 user samples

Flow cell priming and loading

Configuring and running the GridION

Introduction to basecalling, analysis tools, and resources

6 included flow cells

2 included kits (user selected choice)

Contractors will come onsite for training after coordinating dates with research end users, training to be held Monday-Friday between the hours of 8am-4pm. Contractors will not attempt to schedule training on outside of previously mentioned hours, on weekends or the following holidays:

New Year s Day (January 1), Birthday of Martin Luther King, Jr (Third Monday in January), Washington's Birthday (Third Monday in February), Memorial Day (Last Monday in May), Juneteenth National Independence Day (June 19), Independence Day (July 4), Labor Day (First Monday in September), Columbus Day (Second Monday in October), Veterans Day (November 11), Thanksgiving Day (Fourth Thursday in November), Christmas Day (December 25)

SERVICE and WARRANTY: Purchase to include 1 year full warranty and additional 2 year warranty for three (3) total years of coverage for each device. Warranty should include software updates upon release, hardware updates upon release, and return and replace policy.