Updated Statement of Work.pdf

STATEMENT OF WORK (SOW)

Project: Next-Generation Sequencing Services

GENERAL INFORMATION

1.0 Scope of Work:

To conduct shotgun metagenomic sequencing of the microbiome associated with the pest insect Drosophila suzukii. In addition to the sequence information the servicer will provide bioinformatic analyses in which they create a pan-metagenome. They will remove reads from the reference genome of D. suzukii to separate, close the genomes of resident microbes and provide comprehensive metagenomic bioinformatic analyses.

2.0 Background:

Comprehensive metagenomic bioinformatic analyses will provide full shotgun metagenomic sequencing and a custom bioinformatic pipeline that will further and enhance current research at the USDA-ARS, Biological Control of Insects Research Laboratory in Columbia, Missouri.

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements/Tasks: Scope of Work:

Metagenomic sequencing:

Conduct “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; library preparation; bioinformatic analyses of 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 200 samples during year one and in option year two, if elected

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 assembly; bioinformatic analyses of 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, , correlation analysis (as applicable), differential expression analysis (as applicable), enrichment analysis, protein interaction analysis

The servicer will remove reads from the reference genome of D. suzukii to separate and close the genomes of resident microbes. Further, they must perform analyses including but not limited to, data sanitation, metagenomic assembly, core -pan genome analysis, gene number analysis, taxonomic analysis. Further analyses include, but are not limited to Quality report, FASTQ files, data QC, Azenta/GENEWIZ dynamic exploration of microbial taxonomy and abundance, cross-sample comparisons. Pan-metagenome data sanitation. Metagenomic assembly. BLAST assembled contigs for summary hits. NMDS, Krona, Abundance heatmap and Metastats.

Azenta is the only servicer that is capable and willing to do all of the bioinformatics analyses requested using the specified pipelines. Chief among these is to create a true pan-genome of all in a manner that pools the reads from all of the flies and then creates a reference database for each fly. Competitors would not be able to do the same analyses yet would charge 2 to 5 times as much.

The service provider is expected to complete bioinformatic sequencing services as described above for a minimum of 1 and a maximum of 200 samples during year one and in option year two, if elected

4.0 Government Furnished: Not applicable.

5.0 Key Deliverables:

For all sequencing services (genomic, 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. The servicer will also provide the FASTQ files from the sequencing, fully annotated pan-metagenomes and individual fly metagenomes with genome feature files, as well as De Bruijin assemblies at different k-mer lengths. In addition to this, they will include taxonomic analyses which are normally a separate bioinformatic package. They will pull the full amplicon information from the closed genomes and identify individual amplicon sequence variants (this is why the term amplicon was used previously) for each type of organism (flies, viruses, bacteria, fungi). They will then provide the abundance information and detailed reports including but not limited to NMDS, Krona, Abundance heatmap and Metastats.

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. The servicer will also provide the FASTQ files from the sequencing, fully annotated pan-metagenomes and individual fly metagenomes with genome feature files, as well as De Bruijin assemblies at different k-mer lengths. In addition to this, they will include taxonomic analyses which are normally a separate bioinformatic package.

They will pull the full amplicon information from the closed genomes and identify individual amplicon sequence variants (this is why the term amplicon was used previously) for each type of organism (flies, viruses, bacteria, fungi).

They will then provide the abundance information and detailed reports including but not limited to NMDS, Krona, Abundance heatmap and Metastats.

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

6.0 Travel: Not applicable.

7.0 Contractor’s Key Personnel: Not applicable.

8.0 Security Requirements: Not applicable.

9.0 Data Rights: Not applicable.

10.0 Section 508 – Electronic and Information Technology Standards:

Not applicable.