B08_Attachment_A_-_Statement_of_Work_0001.pdf

Statement of Work – Next Generation Sequencing Services: Metagenomics, Whole Genome Sequencing, and RNA-sequencing

GENERAL INFORMATION

A. INTRODUCTION

The USGS Upper Midwest Water Science Center’s (UMid-WSC) Michigan Bacteriological Research Laboratory (MI-BaRL) conducts state-of-the-art microbiology research in association with the Great Lakes Restoration Initiative (GLRI) and USGS Programs such as the Environmental Health Program and the National Water Quality Program. The MI-BaRL needs an experienced next generation sequencing provider for metagenomics, whole genome sequencing (WGS), and whole transcriptome shotgun sequencing or RNA-sequencing (RNA-seq) services to continue to produce consistent, quality, cutting-edge science.

B. PROJECT BACKGROUND

The MI-BaRL is involved in microbial research on a variety of topics including bacterial pathogens, harmful algal blooms (HABs), microbial ecology of contaminated environments, antibiotic resistance, and microbial source tracking. Several of MI-BaRL’s research studies incorporate next-generation sequencing methods to better understand the microbial community and its response in contaminated environments and with harmful bloom formation. USGS microbiologists are incorporating metagenomic profiling (shotgun metagenomic sequencing) and/or whole genome sequencing (WGS) to address not only “who’s there?” but also what these bacteria (isolates with WGS, and communities with metagenomics) may be doing (metabolic capabilities and function). Other projects plan to use whole transcriptome shotgun sequencing or RNA-sequencing to delve deeper and assess gene regulation of key genes associated with nutrient cycling, antimicrobial resistance, pathogenicity, cell protection, and cell lysis.

C. SCOPE

Services, non-personal, to provide all equipment, labor, travel, and supplies and materials (unless otherwise provided herein) necessary to provide shotgun metagenomics sequencing, whole genome sequencing, and RNA sequencing services.

D. PROJECT SPECIFICATIONS AND ASSOCIATED COSTS

The MI-BaRL staff will be responsible for extracting DNA and RNA from all samples, quantifying DNA and RNA concentrations as appropriate, and submitting all administrative paperwork and samples to the contractor (next generation sequencing provider). The MI-BaRL has several ongoing projects that require next generation sequencing services. These projects vary with sample size, number of sequencing runs needed, and type of sequencing technology required (Illumina; AVITI;

Oxford Nanopore; and PacBio). Several of these projects are multi-year projects and to ensure consistency and data quality on these projects, analyses shall be performed by the same contractor.

TECHNICAL REQUIREMENTS

The contractor shall:

1. Complete library preparation (barcoding (tagging) as required to run multiple samples together on an individual sequencing runs, normalization, quantitation, and pooling of product) according to documented lab quality control (QC) guidelines.

2. Perform quality control checks following library prep and prior to sequencing analysis. The USGS may decide to proceed with sequencing of these samples after understanding and acknowledging that these samples have reduced quality. USGS should be notified of quality control issues no later than 30 business days after receipt of samples.

3. Analyze samples and provide sequencing data using Illumina, AVITI, Oxford Nanopore, or PacBio as specified per project requirements determined by USGS Technical Liaison).

4. Provide demultiplex and raw sequencing data for all data.

5. Ability to provide or recommend computational and bioinformatic analyses including customized analysis pipelines for targets genes of interest for data including bacterial genome assembly, transcriptome assembly and variant analysis, and comparative genomics.

6. Notify USGS regarding any samples that do not pass quality control checks following library prep, prior to sequencing, or after sequencing analysis.

7. Deliver data no later than 60 business days following receipt of samples for library prep. Data should be accompanied by a spreadsheet listing sample identifiers, sample barcodes, number of reads, read quality scores, % of read quality scores over a score of 30, and yield (Mbp).

The overall % of quality scores over a score of 30 should be 75% per sequencing run. The contractor shall provide the USGS with access to an FTP server or other secure server for downloading sequencing data. For large amounts of data, an external hard drive with all sequencing data should be provided. All corresponding quality control information including barcodes (tags), library prep kit information, and primers (as appropriate) should be accompanied by data delivery whether through FTP server or external hard drive. Provide access to data for downloading for at minimum 60 days following receipt of sequencing data.

8. Provide a written document describing the methods used for all processes including from library preparation through sequencing and provide all details on reagents, kits, and equipment used. This document is to be provided with data no later than 60 days following receipt of samples for library prep.

GENERAL REQUIRMENTS

The contractor shall:

1. Provide consultation services when planning experiments including guidance for selecting the appropriate sequencing technology and experimental design to best meet research objectives. Consultation services include but are limited to providing information on available sequencing technology and technical requirements and providing answers to questions regarding sequencing services.

2. Provide answers to technical questions regarding sequencing methods used and in regard to technical issues with sequencing data.

3. Provide a Web-based LIMs system that allows the USGS to upload sample information for sequencing.

4. Provide access to an FTP server or other secure server for downloading sequencing data or provide data on an external hard drive.

5. Provide bioinformatics assistance and workflow solutions for sequencing data.

SUPPORTING INFORMATION

Period of Performance:

The contractor shall deliver data no later than 60 days following receipt of samples. Samples will be delivered to the contractor between date of award and September 30, 3031.

USGS QUALITY ASSURANCE SURVEILLENCE PLAN

The USGS Technical Liaison (TL) will assure that the contractor delivers the quality products and services described. The TL will monitor all aspects of the services performed by the contractor.

Substandard Services, services that fall short of the described standards, shall be re-done by the contractor at no additional cost to the Government within 30 days of identified issue.

The Government may seek consideration for more than 2 sequencing failures per year.

SUPPORTING INFORMATION