Statement of Work.docx

Genome Assembly Required Specifications

The service provider will use samples of four wild Hordeum species or wild barley species (Hordeum pusillum Nutt., Hordeum bogdanii Wilensky, Hordeum marinum Huds. subsp. gussoneanum (Parl.) Thell. and Hordeum brachyantherum Nevski subsp. californicum) to generate assembled genomes of four wild barley species including make Omni-C libraries with 15X coverage per haplotype, sequence ~2M PE75bp reads and map the data back to the draft assembly to assess library quality, sequence each library to a target depth of 15X per haplotype of PE150 reads and assemble the genomes by combing Omni-C data sets and long-read data sets generated by the barley group at USDA ARS in Aberdeen Idaho.

The service provider will deliver the results files electronically via secure FTP. The results will consist of:

· HiRise Assembly deliverables:

· The HiRise assembly in FASTA format

· A report summarizing key assembly statistics, features of the Omni-C library, and a linkage density plot of the proximity ligation library data

· A table detailing the breaks made to the input scaffolds

· A table describing the position of the input assembly scaffolds within the final HiRise scaffolds

· BAM file(s) containing alignments of the Omni-c library read pairs mapped to the draft assembly

· TAD Analysis deliverables, if applicable:

· TAD calls at 10kbp, 25 kpb, and 50 kpb

· CTCF binding sites

· A/B compartmental organization

· Isochor locations

· Guide to loading and viewing data in HiGlass

· Summary report

· QC report

· Raw ILMN data from deep sequencing the Omni-C library

· Assembled genomes of four wild barley species (N50 > 100kb)