Genomic Sequencing

This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued. This is a not a total small business set-aside. This solicitation number is RFQ-014-4232-10 and solicitation is issued as a request for quotation (RFQ). The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-38. The United States Department of Agriculture (USDA) Agricultural Research Services (ARS) United Stated Horticultural Research Laboratory (USHRL) has a requirement for production by sequencing of a 500 Mb genome. De Novo Genome Sequencing Needs: Sequencing time- from receipt of samples to completion, within 20 working days. Quality Control- Integrated quality control steps upon first-base incorporation ensure DNA sequence quality. Equivalent quality similar to each channel in the 8-channel flow cell systems which can generate 30-40 million paired-read tags that pass filtering with two or less mismatches. Production equivalent to The Genome AnalyzerIIx which can generate > 27.5 (and up to 33) gigabases of high-quality DNA sequence data per paired end flow cell and >75% of bases with Q ? 30 (2 - 100 bp read, allowing for filtered reads with two or fewer errors). Sequencing Accuracy- Raw read accuracy > 98.0% (averaged over the read) without using a reference sequence to correct errors for 2 x 100 bp reads. Raw read accuracy > 99.0% (averaged over the read) without using a reference sequence to correct errors for 2 x 50 bp reads. Consensus accuracy of 99.999% at less than or equal to 3 coverage in a monoploid organism. PhiX sequence data, using either single or paired-end reads, > 70% (of the reads that pass spectral cross-talk filters) without errors when compared to a PhiX reference sequence for a 100 bp read. Ability to produce a minimum of 2.9 Gb of high-quality filtered bases per day on the sequencer (2 x 100 bp reads, allowing for filtered reads with two or fewer errors). Paired-End Read Support Proof of ability to produce unique combination of paired-end insert size ranges (see publication request): 200-500 bp (short insert paired-end) 2-10 kb (long insert mate pairs) Ability to Handle Low Sample Inputs <1 ?g DNA for genomic DNA sequencing applications (as low as 100 ng for many genomic DNA samples) As low as 10 ng DNA for ChIP-Seq applications <1 ?g total RNA for small RNA sequencing applications <1 ?g Total RNA for mRNA-Seq applications (as low as 100 ng for many Total RNA samples) <1 ?g DNA for bisulfite-converted DNA sequencing applications Data Analysis Software Have a suitable analysis pipeline. Similar to, but not limited to, The Genome Analyzer Analysis Pipeline, which can align reads to a reference sequence and allows the flexibility to recall bases for specialized applications. A pipeline software which provides a graphical user interface to remotely manage the analysis of data using the pipeline software. Software which produces consensus SNP calls and RNA counts for aggregated data from many lanes of multiple flow cells. Similar to The Consensus Assessment of Sequence and Variation (CASAVA). Genome software which provides a single, intuitive, graphical environment for analyzing data from a variety of sequencing and microarray applications including: DNA resequencing ChIP sequencing mRNA sequencing and transcriptome profiling Array-based DNA copy number analysis Array-based gene expression Genotyping Customer-demonstrated applications with peer-reviewed publications: Whole-genome resequencing Targeted resequencing including, but not limited to the following methods: Agilent Sure Select Microarray pull out (Agilent or Nimblegen arrays) Long-range PCR Molecular Inversion Probes De novo sequencing De novo SNP discovery sequencing ChIP-Seq of sequence specific DNA binding proteins ChIP-Seq of histone modifications and epigenetic marks Sequencing of bisulfite-treated DNA to study DNA methylation Metagenomics Full transcriptome analysis Full-length mRNA sequencing Tag-based gene expression Small RNA profiling and discovery Ribosome profiling DNAse 1 hypersensitivity site mapping Nucleosome positioning and chromatin structure studies CLiP-Seq: studying sequence specific protein-RNA interactions CNV-Seq: measuring copy number variation with sequencing GRO-Seq: studying RNA polymerase initiation events Offers will also be evaluated on best value in relation to price. Quotations are to be sent electronically to contact@example.gov. Offerors must include a completed copy of the provision at 52.212-3, Offeror Representations and Certifications Commercial Items, with its offer. Clause at 52.212-4, Contract Terms and Condition Commercial Items, applies to this acquisition. Clause at 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders Commercial Items, applies to this acquisition.