Attachment 1 - Technical Specifications.pdf

Attachment 1

Technical Specifications for Insect Genome Assemblies

Center for Grain and Animal Health in Manhattan, KS requires an acquisition for service to take a draft assembly of long read data from insects (referred to as "contigs") into longer fragments referred to as "scaffolds" that will represent chromosomes from the insect. The data needs to be accurate so that chromosome-scale scaffolds can be obtained. Omni-C technology will scaffold and phase insect genomes on a Hi-Rise platform for optimal genome scaffolding.

OmniC is required to get even whole genome coverage and adequate SNP coverage for phasing to chromosome scale. ARS has used this technology for previous insect genome assemblies, and because the data will be used in a comparative genomics study with previous and current data comparisons, consistency is needed in the approach.

Requirement:

• Scaffolding for four insect genome assemblies using Omni-C technology that uses DNaseI to digest chromatin and not traditional restriction enzymes typically used in Hi-C methods.

• Omni-C libraries will be made and first evaluated by preliminary sequencing.

• Once they pass QC, libraries will be sequenced to 15x coverage for each genome.

• Data will then be assessed with Omni-C kmers and Merqury so that we have an assessment of assembly completeness and accuracy.

• Omni-C kmers will be evaluated for genome size in Genomescope.

• Each insect draft assembly will be assembled with Omni-C data in HiRise to provide haploid-resolved chromosome-scale reference genomes.

• These are absolute requirements since we have previous assemblies based on these methods and we need consistency in the assemblies for comparative genomics.