Genotype-by-Sequencing(nGBS)

Notice of Intent - The USDA, ARS, SEA intends to award a sole source procurement to LGC Genomics GmbH, Inc., Ostendstra'e 25, 12459 Berlin, Germany as they are the sole source for this type normalized genotype-by-sequencing (nGBS) pursuant to the authority of 41 U.S.C. 253(c) (1) and FAR 6.302-1, Only One Responsible Source and No Other Supplies or Services Will Satisfy agency Requirements. The award will be for normalized genotype-by-sequencing (nGBS) of 432 soybean (Glycine max) samples including post-sequence bioinformatics processing. nGBS is a proprietary product of LGC Genomics and for which they are the sole provider. Samples will be processed as library preparation, sequencing, and GBS analysis utilizing nGBS with MslI and the illumina NextSeq (2 x 150 bp) sequencing. Specific steps include 1. Generation of FastQC reports in order to check the quality of sequenced reads, 2. Clipping of sequencing adapters from 3' ends of reads, 3. Restriction-enzyme filter of reads, 4. Alignment against the soybean reference genome reference, 5. SNP calling and genotyping with Freebayes, 6. Custom (n)GBS/ddRAD filtering of SNP calls, 7. sequence tag clusters in FASTA format, 8. Alignment files in SAM/BAM format, 9. VCF formatted files with raw and filtered SNP calls, 10. MS Excel spreadsheet with genotypes and read counts for all samples, and 11 Must have appropriate licenses for all procedures, specifically GBS. LGC Genomics is the sole source for this service that satisfies all of these criteria and meets the requirements of our research. The Government intends to award a firm fixed price Purchase Order on or about November 17th, 2016, using Simplified Acquisition Procedures. This Notice of Intent is not considered a Request for Quotation (RFQ) nor is it a Request for Proposals (RFP). No solicitation document is available and telephone requests will not be honored. Interested persons may identify their interest and capability to respond to this requirement. A determination by the Government not to compete this proposed contract based on responses to this notice is solely within the discretion of the Government. The Government will consider all responses received by 4:00PM central time, November 16th, 2016. Information received will be considered solely for determining whether to conduct a competitive procurement. Inquiries should be mailed to the Contracting Officer at the following address: Contracting Office Address: USDA-ARS P.O. Box 225 141 Experiment Station Road Stoneville, MS. 38776-0225