Notice ID: 1096493-SS Description The United States Department of Agriculture (USDA), Agricultural Research Service (ARS) is searching for firms who can provide Soft ware Development and Data Analysis inSupport of Trait analysis by Association, Evolution, and Linkage (TASSEL) andthe Practical Haplotype Graph (PHG) to develop genomic databases. The work involves supporting the maintenance and development of software developedby the project “Improving Crop Eff iciency Using Genomic Diversity andComputational Modeling” (8062-21000-043-000-D) and providing analytical support for genetic and bioinformatic analysis. Background: The United States Department of Agriculture (USDA) Agriculture Research Service (ARS) Office of the Chief Information Officer (OCIO) requires contractor assistance. The solution shall include: • Optimize and deploy the PHG's Kmer based read mapping approach so that it uses one-fifth the memory of the current pipeline that relies on MiniMap2. • Optimize and deploy the Diploid and Haploid Path finding algorithms in the PHG specifically targeting sorghum, cassava, rice and cowpea.  Code and algorithms will need to be generalized to account for a wide range of recombination and heterozygosity patterns found in these species.  By the end of the contract, path finding will be done for each species’ PHGs. • Integrate these and any additional improvements with the Genomics Breeding Hub for data and analysis as applicable.  This will include developing new User Interfaces, TASSEL Plugins, sample Jupyter notebooks and APIs to allow for seamless access and use of these algorithms and tools by users of the Genomics Breeding Hub. • Implement haplotype based genome wide association algorithm in TASSEL6 and associated rTASSEL. • All software and related documentation will be delivered to the project’s Bitbucket repository. Commits to the repository will provide sufficient documentation of the contractor’s deliverables. Bitbucket is a secure, commercial concurrent versioning system for tracking software and document changes. Submitted software must be reviewed and approved by the project’s programming team. In addition, tasks are to be tracked in the project Trello board. Trello is a project tracking system. Read more here.