1.W81XWH18R0069_PWS.pdf

Performance Work Statement (PWS)

Longitudinal study of dehisced wound metagenomics

Vision Statement (United States Army Institute of Surgical Research) (USAISR)

The USAISR Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate mission is to provide militarily relevant research and solutions for the prevention and rehabilitation of craniofacial trauma and infections dental diseases.

1.0. Introduction

The USAISR is part of the U.S. Army Medical Research and Materiel Command. The USAISR is dedicated to both laboratory and clinical trauma research. Its mission is to provide requirements-driven combat casualty care medical solutions and products for injured soldiers from self-aid through definitive care across the full spectrum of military operations; provide state-of-the-art trauma, bum, and critical care to Department of Defense beneficiaries around the world and civilians in our trauma region; and provide Burn Special Medical Augmentation Response Teams.

1.2. Background

The USAISR mission is to be the nation’s premier joint research organization planning and executing registry-based and translational research providing innovative solutions for burn, trauma, and combat casualty care from the point of injury through rehabilitation. This non personal based service contract will provide the USAISR with the required resources to staff and maintain mission critical operations. Failure to provide the support services needed to carry out and complete routine requirements would be extremely detrimental to the mission.

The USAISR Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate has a need for Next Generation Sequencing (NGS) services using latest deep-sequencing, high-throughput, HiSeq NGS technology for whole-genome shotgun sequencing (metagenome) of viral (bacteriophage and mycophages), fungal, and bacterial communities residing in the post-surgery dehisced wounds collected longitudinally from participating subjects. Prior expertise and proficiency in similar studies to generate high-quality sequenced reads with sufficient sequenced read length and coverage for downstream computational analyses are required. In addition, a proficient bioinformatics team with expertise in assembly, annotation, and analysis of fungal, viral, and bacterial whole-metagenome sequences for the timely completion of downstream computational analyses for the different tasks described below is required.

1.3. Scope of Work

1.3.1. This PWS contains no services that are inherently governmental functions, as defined in FAR Part 2.1. The Government shall neither supervise contractor employees nor control the method by which the contractor performs the required tasks. Under no circumstances shall the Government assign tasks to, or prepare work schedules for, individual contractor employees. It shall be the responsibility of the contractor to manage its employees and to guard against any actions that are of the nature of personal services, or give the perception of personal services. If the contractor believes that any actions constitute, or are perceived to constitute personal services, it shall be the contractor's responsibility to notify the Contracting Officer (KO) immediately.

The goal of this study is to apply a high-resolution metagenomics approach towards specimens (wound wash, wound swab, and sharp debridement) collected longitudinally from surgical dehisced wounds for identification (bacteria, archaea, fungi, and viruses) and molecular characterization of the microbial ecosystem (e.g., virulence and network profile) present in healing versus healing-impaired dehisced wounds collected from 90 patients over a period of 26 weeks. Furthermore, the microbial profile of these wound specimens, which target different ecosystems of the wound (viable and non-viable tissue), will be computationally correlated with the wound etiology and clinically-relevant metadata (e.g., surgery conditions and comorbidity) of enrolled participants. Defining the microbial composition and genotypic profiling of healing and non-healings dehisced wound residents via microbial surveying (bacterial 16S rRNA and fungal ITS2 rRNA) and via high-throughput deep whole-genome sequencing (bacteria, fungi, archaea and viruses) will aid in identifying metagenomics clinical biomarkers and molecular crosstalk between wound inhabitants that may ultimately lead to changes in survival, virulence, and disease outcome; thus providing the foundation for understanding the homeostatic state and mechanisms contributing to the development of healing and non-healing wounds. Moreover, identifying the genotypic features of a large collection of healing and non-healing dehisced wounds collected on weekly/bi-weekly basis in a longitudinal manner can ultimately lead to novel clinical diagnostics (e.g., biomarkers that predict healing versus non-healing wounds) or improved treatment strategies (e.g., wound community exploitation to improve outcome).

1.4. Organizational Conflicts of Interest (OCI)

1.4.1. The USAMRMC has categorized all service procurements into one of the following three categories as defined below, for the purpose of identifying, avoiding or mitigating Organizational Conflicts of Interest (OCI) in accordance with (IAW) Federal Acquisition Regulation (FAR) Subpart 9.5. These categories are defined as follows:

Category 1: Command Wide Internal Support: Services which, by their very nature, give the Contractor access to non-public procurement sensitive data about the contract requirements, other contractors’ proprietary information, or put the contractor in a position to influence the award decision on a contract in which they are participating. Services would be characterized as having access to Command Wide procurement sensitive information, or work that could likely have an influence over follow-on awards or contracts with subordinate directorates/Commands.

Category 2: Program Management Support: Services which assist USAMRMC in planning and managing an organization’s activities and programs. These include, for example: requirements analysis, acquisition support, budget planning and management, business process reengineering, program planning and execution support, and independent technical management support. Services would be characterized as having access to only Directorate or Subordinate Command level procurement sensitive information or work that would have little influence on follow-on requirements or requirements of other directorates/Subordinate Commands.

Category 3: Product Support. Services or end items required to meet the mission requirements of the organization’s activities and programs. These include, for example: concept exploration and development, system design, system development and integration, COTS procurement and integration, internal development testing, deployment, installation, operations, and maintenance. Services can be characterized as having little or no access to procurement sensitive information other than the immediate requirement and little chances of follow-on work that can be influenced by the immediate requirement.

1.4.2. OCI Certification. USAMRMC OCI Category 3 is applicable for this acquisition.

1.4.2.1. The Contractor shall perform a thorough comparative analysis of the potential new work against all current and previous works performed in support of the USAISR organization and ascertain whether they have a possible conflict of interest. If there is a conflict of interest or the appearance of a conflict of interest, the Contractor shall provide a comprehensive OCI Mitigation Plan (See PWS Section 5.1). The Contractor shall complete the OCI Certification at time of proposal submission.

2.0. Performance Requirements

(a) The Contractor shall provide a workforce possessing the skills, knowledge and training to satisfactorily perform the services required under this contract. The Contractor shall accomplish the assigned work by employing and utilizing qualified personnel with the appropriate combinations of education, training, and experience. The contractor shall match personnel skills to the work or task with a minimum of under or over employment of resources.

(b) The Contractor shall submit invoicing through Wide Area Work Flow (WAWF). The Government will review monthly performance, and will attend regular task performance review meetings with the Contractor to survey quality of products and services according to the Quality Assurance Surveillance Plan (QASP).

(c) The place of performance for the required tasks shall be at the contractor’s facility. The period of performance shall not exceed two years.

2.1 First Year of the Dehisced Wound Microbiome Project

2.1.1 Patient Eligibility and Enrollment: The contractor shall partner with a hospital that is capable of enrolling 90 patients presenting with dehisced wounds within first year of study. Furthermore, the hospital must have the necessary number of clinics, staff, physicians, and surgeons that can commit to manage patient qualification, specimen collection and delivery for each designated patient visit within the 26 week enrollment period.

2.1.2 Generation of Longitudinal Study Documents:

2.1.2.1. Eligibility Criteria: The eligibility criteria for this study requires patients to be more than 18 years of age (male and female). Patients can be of any ethnicities. Qualified patients must be diagnosed and seen for dehisced wound-care within 10 days of wound occurrence. Patient exclusion criteria includes individuals under 18 years of age and based on co-morbidities including but not to limited to immunodeficiency disorders and diseases that influence wound healing (e.g., HIV and cancer).

2.1.2.2. Consent form: The contractor shall ensure participating patients consent to enroll in the study for 26 weeks and attend every scheduled doctor visit for specimen collection. A patient consent form must instruct the patient to avoid using topical antibiotics cream and antimicrobial soap on the wound 24 hours prior to scheduled visit. Patients shall consent to having the following specimens collected: drainage from routine wound wash, swabs of the wound area and healthy skin (contralateral if applicable and only during the first patient visit), debrided non-viable wound tissue when needed (sharp debridement is preferred), and swabs of the wound post-debridement. The patient shall be notified in the consent form that the collected specimens will be non-identifiable by researchers at ISR and are used for identification of dehisced wound microbial communities. The patient shall authorize the biobanking of their specimens indefinitely at ISR for microbiological research.

2.1.2.3. Study-related Standard Operational Procedures (SOP)s: In collaboration with ISR scientists, the contractor must generate study-related SOPs prior to start of the study. The SOPs shall include instructions for a) patient qualification, consent, scheduling; b) Specimen handling, collection, and delivery. The SOPs will be approved by both ISR and contractor personnel.

2.1.3. Patient Enrolment and Specimen Collection. The contractor shall conduct and provide ISR with a feasibility assessment of the network of wound clinics, clinicians, and patient size to be considered for this study.

The assessment must include types of dehisced wounds and the number of patients treated for dehisced wounds annually (for the past 3 years) and the percentage of patients healing before 13 weeks and between 13 and 26 week of being diagnosed and treated for dehisced wounds. To ensure enrollment of 90 patients, multiple clinics and physicians can be involved in this study; however, the contractor shall provide the necessary staff for coordination and management of the study between the different clinics and physicians to ensure proper scheduling, specimen collection and delivery in an efficient and timely manner.

2.1.3.1. Patient Enrollment: A total of 90 patients of different gender, ethnicity, and age (over 18 years of age) can be enrolled in this longitudinal study. Patient enrollment and specimen collection must be complete in a one year time period. At the end of the collection period, the contractor shall have collected 2,980 wound specimens for analysis.

2.1.3.2. Specimen Collection: During the 26 week study period, the contractor shall manage patient unidentifiable code and associated key, patient scheduling and visits (a total of 11 visits per patient) to coordinate specimen collection and delivery. Wound specimens shall include collection of drainage from wound wash, wound swabs (pre- and post-debridement), and wound debridement (when needed). All of the specimen collection procedures will follow the IRB and the SOP.

2.1.3.3. Patient Metadata: During patient visit, the contractor shall capture an image of the dehisced wound and populate the clinically-relevant metadata questionnaire that will be provided to ISR for down-stream study analyses.

2.1.3.4. Specimen Storage: Specimens shall be stored immediately on ice and delivered within three hours of specimen collection.

2.1.3.5. Specimen Delivery: The hospital must have an organized system in place that will smoothly coordinate patient qualification, scheduling, specimen collection and delivery to the contractor to aid in proper processing of specimens upon delivery. If multiple clinics and physicians are involved, the hospital management staff must ensure efficient and timely specimen delivery.

Deliverables. Deliverables must meet accepted industry standards and meet the requirements set forth in contractual documentation. The contractor will be responsible for delivering/accomplishing all end items specified.

Number Deliverable Title Due Date

Generate necessary study documents including approved IRB by the local collection site(s) and the US Army Medical Research and Materiel Command, Human Research Protection Office, eligibility criteria, consent forms, study SOPs as mentioned in PWS 2.1.1.

Within first year of contract

Enroll total of 90 qualified patients (11 visits per patient) into the longitudinal study of 26 weeks as mentioned in PWS 2.1.3.

Within first year of contract

Collect necessary information and specimens from 90 patients in a period of 26 weeks as mentioned PWS 2.1.3.

Within first year of contract

Provide output sequenced reads (raw and filtered), conduct assembly, annotation of 2,980 (16S/ITS2) amplicons sequenced read files as described in PWS 2.2.

Within first year of contract

2.2 Microbial Survey Study of 2,980 Wound Specimens.

The contractor personnel shall be an expert in conducting similar large scale studies based on documented prior experience using high-resolution, high-throughput MiSeq and HiSeq technologies and applicable computational tools.

2.2.1. Key Task 1: To perform microbial survey of the skin fungal and bacterial residents, the contractor shall use high-throughput NGS MiSeq technology to conduct amplicon sequencing of hypervariable regions of ribosomal RNA (rRNA)-encoding genes for classification of taxonomy (operational taxonomic unit, OTU) and measurement of biodiversity and abundance of the fungal (internal transcribed spacer, (ITS2)) and bacterial (16S rRNA) populations residing in the healing and non-healing wounds. The Government requires the resulting 16S or ITS amplicon sequence file for each skin sample to be at least 100,000 sequenced reads per sample. The details of the capabilities and approaches for amplicon library preparation and NGS sequencing shall be provided in detail by the contractor and discussed with the ISR investigators.

The contractor shall use established and published pipeline including but not limited to QIIME, PIPITS, MICROPITA and PICRUSt for downstream analysis. Deviation from these approaches requires detailed scientific explanation by the contractor and approval by the Contract officer representative (COR).

Deliverable: The 16S or ITS amplicon raw and processed sequence file for each skin sample must yield at least 100,000 sequenced reads per sample.

2.3. Bacterial survey using 16S rRNA

2.3.1. Key Task 1: The contractor shall use hypervariable region V3-V4 16S rRNA primers, MiSeq NGS library preparation and sequencing methods. Further details including re-sequencing of low read samples and other necessary modifications will be discussed with the COR prior to execution of tasks. The contractor shall use the amplicon library bead-based cleanup approach (e.g., Agencourt AMPure XP beads) instead of gel-purification. The 16S amplicon libraries shall be pooled at an equimolar concentration with no more than 96 samples pooled for a single sequencing run. The contractor shall use MiSeq sequencing chemistry that provides 300bp read length and Paired-End (PE) reads for 600 cycles of amplification that would yield at least 100,000 reads per run for each 16S rRNA amplicon library sample. For sequencing, contractor shall include in each of the sequencing runs a 10 to 20% PhiX in the pooled amplicon library as an internal control and a microbial mock DNA standard.

Deliverables: Sequenced 16S amplicon FASTQ files shall be generated with a sequence depth of 100,000 sequenced reads per sample (not including the PhiX control). Majority of the reads will have a Phred score of >30 and a small percentage of the reads will be of the PhiX Spike-in control.

2.4. Fungal survey using ITS2 rRNA

2.4.1. Key Task 1: The Contractor shall use hypervariable region ITS4-ITS7 (ITS2 rRNA) gene-encoding primers, MiSeq NGS library preparation and sequencing methods. Further details including re-sequencing of low read samples and other necessary modifications will be discussed with the COR prior to execution of tasks. The contractor shall use the amplicon library bead-based cleanup approach (e.g., Agencourt AMPure XP beads) instead of gel-purification. The ITS amplicon libraries shall be pooled at an equimolar concentration with no more than 96 samples pooled for a single sequencing run. The contractor shall use MiSeq sequencing chemistry that provides 300bp read length and Paired-End (PE) reads for 600 cycles of amplification that would yield at least 100,000 reads per run for each 16S library sample. For sequencing, contractor shall include in each of the sequencing runs a 10 to 20% PhiX in the pooled amplicon library as an internal control and a microbial DNA standard.

2.4.1.1. Sub-Task 1: The Contractor shall use the ISR standardized steps for robust ITS2 amplification of fungal genomic DNA (gDNA). The Government will provide assistance and guidance for this workflow to ensure proper enrichment of fungal community of healing and non-healing wounds. Otherwise, steps pertaining to amplicon library generation, cleanup, qualification, and sequencing shall be followed as described in PWS 2.3.1., with the exception of the ITS2 region of fungi. This fungal gene marker exhibits a higher degree of variability of nucleotide length and the contractor shall include no size-selection steps during the generation of the amplicon libraries, except for bead-based cleanup, which removes DNA fragments below 200bp in length.

Deliverables: Sequenced ITS2 amplicon FASTQ files generated with a sequence depth of 100,000 sequenced reads per sample (not including the PhiX control). Majority of the reads shall have a Phred score of >30 and a small percentage of the reads shall be of the PhiX Spike-in control.

3.0 Second Year of the Dehisced Wound Microbiome Project

3.1 Objective 1: Metagenomics Study of 1,490 Wound Specimens Down-Selected from Microbial Survey (2.1).

3.1.1. Key Task 1: The contractor shall use the deep-sequencing high-throughput NGS HiSeq 3000 or 4000 platform technology, conduct whole-genome shotgun sequencing (WGS) to capture and characterize microbial residents of healing and non-healing dehisced wounds including fungi, bacteria, archaea and viruses (ssDNA and dsDNA). The contractor shall provide the details of the capabilities and approaches for library preparation and NGS sequencing and discussed with the USAISR investigators. Deviation from the requested approach requires detailed scientific explanation by the vendor.

3.1.2. Key Task 2: For library preparation, the contractor shall have the expertise and capability to use chemistries specific for low input DNA sample and those that capture ssDNA such as Accel-NGS-1S chemistry. Contractor shall use High-throughput (HiSeq) deep sequencing technology for paired-end (PE) sequencing of wound specimens that provide sequenced reads of at least 200 million reads for each wound specimen to counter host DNA contamination.

Deliverables: Sequenced whole-metagenome FASTQ files shall be generated with a sequence depth of 200 million sequenced reads per sample (not including the PhiX control). Majority of the reads must have a Phred score of >30 and a small percentage of the reads may be of the PhiX Spike-in control. Mock communities shall be used as controls (staggered and even community).

3.2 Objective 2: Amplicon Bioinformatics Analysis

3.2.1. Key Task 1: The contractor shall quality check, filter output sequenced read files (e.g., chimera removal) followed by merging of PE reads.

3.2.2. Key Task 2: For bacterial survey, the contractor shall conduct reference-based (open reference) and de novo sequenced read assembly for bacterial taxonomic classification (operational taxonomic unit for phyla to genus at 97% similarity) using well-established tools such as QIIME with latest Greengenes database.

3.2.2.1. Sub-Task 1: To generate species-level identification with needed accuracy, the contractor shall use tested and published tools such as Bayesian-based taxonomic classification (BLCA).

3.2.3. Key Task 3: For fungal survey, the contractor shall use well-established classification method of PIPITS approach for taxonomic classification of fungi using latest ITS2 database.

3.2.4. Key Task 4: For functional analysis of 16S sequenced FASTQ files, contractor shall normalize sequenced data by copy number per specie using tools such as PICRUSt.

3.2.5. Key Task 5: The contractor shall perform diversity analysis within each sample and community (alpha diversity) and between different samples or communities (beta diversity) using well-established pipelines such as QIIME. For alpha diversity, government requests the use of accepted analyses for species richness (e.g, Chao1), evenness and diversity (e.g., Shannon), abundance (e.g., Simpson), and phylogenetic diversity (e.g.,PD_whole_tree).

For beta diversity analysis, the government requests the use of common pair-wise comparison tools including Bray- Curtis, weighted and unweighted UniFrac matrices.

3.2.6. Key Task 6: The contractor shall predict metagenome functional content and categorize by predicted pathway function (e.g., KEGG and COG) of each sequenced sample using tools such as PICRUSt followed by comparison of different metadata variables (e.g., healing versus non-healing). For analysis of inter-domain interaction and combined influence of fungi and bacteria in the microbiome, contractor shall be using tools such as SPIEC-EASI tool.

3.2.7. Key Task 7: The contractor shall perform identification of “core” microbiome (in 100% and 50% of samples for community if interest), keystone species (hubs), and calculate group significance and category comparisons using appropriate tools available through QIIME.

3.2.8. Key Task 8: The contractor shall conduct association study to correlate the microbial survey with clinical metadata and identify possible markers that are predictive of disease phenotype and outcome (e.g., Random Forest Classifier and LefSe).

3.2.9. Key Task 9: The contractor shall, while using computational tools such as MICROPITA, down size the number of study specimens by the following categories: identify samples that exhibit maximum diversity, samples with specific microbiomes that represent targeted phenotype (e.g., healed versus non-healing wound), samples with most dissimilar microbiome or at the border of the phenotype, and samples dominated by a specific microbe (fungi or bacteria).

3.2.10. Deliverables 1. Contractor shall provide taxonomic identification profile of each wound specimen and microbiome community. Contractor will identify microbial community similarities or differences using specified alpha and beta diversity analyses between different a) individuals, b) wound types, c) time points (patient visit). The core microbiome of each microbial community shall be calculated and provided for 100% and 50% community membership as well as potential key-stone species of healing versus non-healing wound. Functional analysis of healing and non-healing wound microbiome will be presented in the form of network topology (e.g., SPIEC-EASI), heatmaps or bar charts of predicted functions and community contributions (e.g., PICRUSt), MICROPITA analysis will provide the government with data in the form of dot plots and multi-dimensional scale plots that visualize the grouping of specimens based on their respective metadata and allow the down-selection of samples for down-stream analyses. All of the generated data will be provided along with the underlying computational code as raw/source file and in the form of an appropriate presentation figure that can be published (e.g., bar charts, multidimensional plot, networks).

3.3. Objective 3: Metagenomics Bioinformatics Analysis

3.3.1. Key Task 1: The contractor shall trim and filter output sequenced read files followed by reference-based and de novo sequenced read assembly using custom-curated databases constructed from latest available sequencing databases.

3.3.2. Key Task 2: The contractor shall remove any human DNA carryover using in-silico tools previously tested and published for proper level of stringency and accuracy for human DNA.

3.3.3. Key Task 3: The contractor shall conduct metagenome profiling of microbial community (Bacteria, viruses, archaea, and fungi) using high resolution tools to reach species-level identification such as MetaPhlAn2.

3.3.4. Key Task 4: The contractor shall conduct gene prediction and annotation of assembled contigs for fungi, bacteria, archaea, and viruses; create necessary documents and figures that display annotations of each sample separated by kingdom. In the case of un-annotated genes, perform prediction of gene function using available databases.

3.3.5. Key Task 5: The contractor shall identify differentially abundant genomic features (pathway, genes, or taxa) and potential biomarkers associated with specific wound phenotypes and wound-metadata variables using tools such as LDS Effect Size (LEfSe).

3.3.6. Key Task 6: The contractor shall conduct comparative genomics of the fungal, viral, archaeal and bacterial sequences for a) each patients during the course of study (26 weeks), b) for patients with the same outcome (healed or non-healed), c) across patients with different wound type, and d) and different patients at the similar time point (e.g., week 3 post-surgery) of healing.

3.3.7. Key Task 7: The contractor shall conduct genotypic profiling and pathogenome characterization of the sequenced data for each kingdom for the presence of known genotypes or genetic features that are associated with factors including virulence, survival, and host-immune evasion. Identify specific genotypes and genetic features that are similar and that are distinct between different patient populations (e.g., healing) and based on available patient metadata.

3.3.8. Key Task 8: The contractor shall identify the significance of similarity or dissimilarity between different patient groups and patient metadata variables, perform well-established metagenomics-related statistical analyses (e.g., Negative binomial mixed model) including but not limited to approaches described by Biobakery package.

3.3.9. Deliverables 1: Contractor shall identify the microbiome community structure (fungi, bacteria, viruses, and archaea) of different wound communities and present the data in terms of community categories and disease outcome. Contractor shall provide figures and lists of potential biomarkers (pathways, taxa, functional categories, keystone species) identified in healing versus non-healing wound microbial community. Contractor shall provide government with genotypic and pathogenome profiles of members of different kingdoms as well as cross-Kingdome talk in the wound microbiome. Comparative metagenomics analysis shall provide the significant differences and similarities between the communities of healing and non-healing dehisced wounds that are categorized as described in PWS 3.2.6.

4.0 Other Requirements

4.1. Government Furnished

4.1.1. The Government will provide samples to contractor to be sequenced.

4.1.2. Property Security: The Contractor employee is responsible for safeguarding all Government samples.

4.2. Proprietary Information Assurance and Security

4.2.1. The contractor shall protect all data in the strictest confidence; prevent the unauthorized duplication, use and disclosure of information that is subject to the Privacy Act of 1974, HIPAA IAW applicable statutory, regulations, local policies and procedures.

4.2.2. For any references regarding USAMRMC procedures regarding HIPAA, PHI and PII, please refer to Chapter

10. The Health Insurance Portability and Accountability Act (HIPAA) of the HQ USAMRMC IRB Policies and Procedures located at http://mrmc.amedd.army.mil/index.cfm?pageid=research_protections.irbo. Additional information regarding ethical principles, federal requirements and guidelines can be located in Appendix A of the same document. For further information, please contact USArmy.Detrick.MEDCOM-USAMRMC.Other.IRB- Office@mail.mil.

4.2.3. All data received, processed, evaluated, loaded, and created as a result of this contract shall remain the sole property of the Government and shall be returned to the Government at the conclusion of the contract, unless the KO grants a specific exception.

4.2.4. The contractor is prohibited from appropriation, disclosure, or unauthorized use of proprietary information that is acquired in the execution of this contract.

4.2.5. Government Data Rights: All products including files, software, and other information, which are created, produced, or developed during the period of performance is the property of the Government and shall be returned unless the Government grants the contractor permission to retain the materials and products for continued development or publication.

5.0. Schedules/Deliverables

Deliverables. Deliverables must meet accepted industry standards and meet the requirements set forth in contractual documentation. The contractor will be responsible for delivering/accomplishing all end items specified.

Number Deliverable Title Due Date

Provide output sequenced reads (raw and filtered), conduct assembly, and annotation of 1,490 whole-metagenomics sequenced read files as described in PWS 3.1.

Within second year of contract

Provide computational analysis for finalized, polished, publication ready results of 2,980 (16S/ITS2) amplicons sequences and data figures of bacterial and fungal microbial survey for diversity and abundance as mentioned in PWS 3.2.

Within second year of contract

Provide computational analysis for finalized, polished, publication ready results of 1,490 metagenomic sequences and figures of metagenomics analyses and data as discussed in PWS 3.3.

Within second year of contract

5.1. Method of Delivery

5.1.1. Electronic copies shall be delivered using Microsoft Office suite of tools (for example, MS Word, MS Excel, etc.), unless otherwise specified by the COR. Electronic submission shall be made via email, unless otherwise agreed to by the COR.

5.1.2. All other items to be delivered will be arranged by the COR.