Attachment 1 Specifications.docx

Statement of work Background USDA-ARS Animal Parasitic Disease Laboratory (APDL) in Beltsville, Maryland has 1,100 samples collected from gut contents of cattle, small ruminants (goats and sheep), pigs, and lab animals. Total DNA has been extracted from these samples. APDL needs single-molecule synthetic full-length based microbiome studies from next-generation sequencing, assembly and annotation, and data analysis to identify biomarkers and molecular signatures for host resilience and gut microbiome restoration.

Requirements These samples will be provided to the vendor in 5 to 9 batches (96 to 192 samples per batch) over the period of 36 months (from Sept 15, 2022 to Sept 14, 2025) in dry ice with overnight express delivery. The full-length amplification and amplicon sequencing will be performed at 150 bp/read (pair-end) using the Illumina platform. The minimum yield will be 10 million pair-end reads per sample with Q30 > 80% with an overall de novo assembly error rate < 2.0%. Among these samples submitted, 1,000 samples will be sequenced, assembled, and analyzed based on the 16S rRNA pipeline, including the dada2 algorithm. The additional 100 samples will be performed using 18S ITS 1 and 2 platforms. Initial analysis services include that the sequence quality check against standard quality control parameters, full-length single-molecule assembly, and annotation against public databases, including both GreenGene and Silva databases. The deliverables will include raw sequences, sequences of assembled and clustered molecules (minimum 10,000 full-length clustered molecule per sample), alpha and beta diversity in tsv or excel format, amplicon sequence variant (ASV) feature tables, count/taxonomy tables (from species to phylum levels), rarefaction curve data, a descriptive summary report, and all intermediate files.

Period of Performance (POP) for the requisition Sept 15, 2022 to Sept 14, 2025