Statement of Work.pdf

Statement of Work (SOW) Next-Generation Sequencing Services

GENERAL INFORMATION

1.0 Scope of Work:

1) To conduct DNA and RNA sample sequencing using next-generation technologies

2) To generate de novo genomic and transcriptomic assemblies of clean nucleic acid sequencing data

3) To conduct metagenomic amplicon sequencing

4) To conduct bioinformatic analyses of nucleic acid sequencing data

5) The services provided under this agreement will have a two year ordering period. Pricing to be provided for 09/01/2023-08/31/2024 and 09/01/2024- 08/31/2025.

2.0 Background:

The objective is the completion of Next-Generation nucleic acid sequencing and bioinformatic analyses that further and enhance current research at the USDA-ARS, Biological Control of Insects Research Laboratory in Columbia, Missouri. These services will accelerate progress on Objectives 1-4 of the in-house project 5070-22000-038-00-D.

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements & Specifications:

• Genomic sequencing:

- Conduct “genome survey” sequencing using the NovaSeq platform.

- 150 bp paired-end sequencing, with a minimum of 24 Gb of raw data per sample.

- Specifications: Service provider to provide sample QC analysis; library preparation; statistical analyses of data production and quality; de novo genomic assembly; bioinformatic analyses of genomic assembly including, but not limited to, K-mer analysis, GC content, repeat content rate evaluation, heterozygous rate evaluation, genome size evaluation, contamination inspection.

- The service provider is expected to complete genomic sequencing services as described above for a minimum of 1 and a maximum of 10 samples.

• Transcriptomic sequencing:

- Conduct “mRNA-seq” sequencing using the NovaSeq platform.

- 150 bp paired-end sequencing, with a minimum of 24 Gb of raw data per sample.

- Specifications: Service provider to provide sample QC analysis; library preparation; statistical analyses of data production and quality; de novo transcriptomic assembly; bioinformatic analyses of transcriptomic assembly including, but not limited to, gene functional annotation using at least seven databases, GO/COG/KEGG classification, CDS prediction, SNP/INDEL calling, SSR analysis, gene expression analysis within and between sample groups, correlation analysis (as applicable), differential expression analysis (as applicable), enrichment analysis, protein interaction analysis.

- The service provider is expected to complete transcriptomic sequencing services as described above for a minimum of 1 and a maximum of 120 samples.

Statement of Work (SOW) Next-Generation Sequencing Services

• Metagenomic sequencing:

- Conduct “amplicon metagenomic” sequencing using the NovaSeq platform.

- 250 bp paired-end sequencing, with a minimum of 0.05 M reads per sample.

- Specifications: Service provider to provide sample QC analysis; PCR amplification; amplicon library preparation; bioinformatic analyses of amplicon sequencing, including but not limited to, data split and reads merging, data quality control, filtration and chimera removal, taxonomic analysis, alpha diversity analysis, beta diversity analysis, functional prediction.

- The service provider is expected to complete metagenomic sequencing services as described above for a minimum of 1 and a maximum of 160 samples.

• Bioinformatic services:

- Conduct de novo transcriptome generation and bioinformatic analyses using previously generated raw nucleic acid sequencing data.

- Specifications: Service provider to provide statistical analyses of data production and quality; data quality control, filtering reads to remove adapters and low quality reads; de novo transcriptomic assembly; bioinformatic analyses of transcriptomic assembly including, but not limited to, gene functional annotation using at least seven databases, GO/COG/KEGG classification, CDS prediction, SNP/INDEL calling, SSR analysis, gene expression analysis within and between sample groups, correlation analysis (as applicable), differential expression analysis (as applicable), enrichment analysis, protein interaction analysis.

- The service provider is expected to complete bioinformatic sequencing services as described above for a minimum of 1 and a maximum of 120 samples.

4.0 Government Furnished:

Nucleic acid samples or raw sequence data.

5.0 Key Deliverables:

• For all sequencing services (genomic, transcriptomic and metagenomic) described above, service provider is expected to:

- Provide client with sample QC analysis and await client approval prior to commencement of sample sequencing.

- Provide client with all raw sequencing data in the form of .fastq files, assemblies in the form of .fasta files, and bioinformatic analysis data in tabulated (e.g., Excel) format.

• For Bioinformatic (only) services described above, service provider is expected to:

- Provide client with assemblies in the form of .fasta files, and bioinformatic analysis data in tabulated (e.g., Excel) format.

• For all services:

- Provide client with access to a web portal through which project forms and reports can be completed and project progress can be monitored.

- Deliver all data and results through a secure, service provider-based File Transfer Protocol server directly to client named on individual project estimate within 35 business days of sample QC approval for sequencing projects, or within 20 business days for bioinformatic analysis projects.