Proximo Hi-C Kit for Fungal Samples

Description

Proximity Ligation NGS Library Prep from crude fungal samples, for Illumina Sequencing.

The Proximo Hi-C method employs cost-effective proximity ligation data generated using in vivo Hi-C to orient and order contigs into chromosome-scale scaffolds and generate reference-quality fungal genome assemblies. Go beyond the sequence to phase haplotypes and detect structural variation; and help deliver on the promise of genomics across a wide range of many applications in agriculture and medicine.

• Scaffold chromosome-scale fungal genomes directly from fungal samples
• No high-molecular-weight DNA extraction required
• User-friendly complete 2-pack Hi-C Kit, including NGS library prep reagents
• Short-read compatible; yields libraries for Illumina® sequencing
• Individualized data analysis packages for fungal genome scaffolding/assembly, haplotype phasing, variant detection, and interaction analyses are available – please contact us to discuss your project details

Proximity ligation (Hi-C) libraries are generated from a crude fungal sample. Interactions are captured by crosslinking, digesting, and creating chimeric junctions that are sequenced. The Hi-C sequence data may be used in conjunction with shotgun/whole genome sequence data obtained by standard NGS approaches for genome assembly and scaffolding, haplotype phasing, detection of structural variants, TAD calling, and other interaction analyses

Unravel the mysteries of the fungal world

Fungal genomes contain challenging elements, such as repeats, duplications and structural elements that complicate both sequencing and assembly. Based on proximity ligation (Hi-C) technology, Proximo enables the untangling of these sticky genomic knots, and shows promise in taming genomes across this diverse and neglected kingdom of life comprising between 2.2 and 3.8 million species.

Proximo Workflow:
The proximity ligation (Hi-C) library prep reagents provide a streamlined protocol that does not require culturing of fungi or extraction of high-molecular weight (HMW) DNA. The processing guidelines ensure robust results. The 8-step library prep workflow can be completed in 2 working days, and requires only 3 hours of hands-on time. The protocol contains several convenient, safe stopping points. Sequencing may be performed on any Illumina® sequencer. The Proximo Kit yields a dual-indexed proximity ligation library, for which ~50 to 100 million paired-end reads are required. For analyzing your Hi-C sequence data, you also need draft assembly sequencing data of your samples, which may be performed with a suitable library preparation kit of your choice – contact us for recommendations or to discuss a service project if you do not have prior experience with shotgun/whole genome library preparation and sequencing.

Data analysis is offered optionally as a customized service, e.g. Phase Genomics´ Proximo Genome Scaffolding platform utilizing a three-stage genome scaffolding algorithm. Hi-C Proximo data may also be integrated with other computational approaches (e.g. FALCON-Phase) to enable the production of “gold” and “platinum” fungus genomes.
The open source software FALCON-Phase combines Proximo data with the high accuracy, long-read sequencing data from PacBio®, enabling researchers to create haplotype-resolved genome sequences on a chromosomal scale.

Please contact us to let us know your project details and receive a quote.