The links below provide access to Phase Genomics' official software & bioinformatics documentation, which includes both instructions on how to perform various computational tasks with Hi-C data generated from our kits, as well as general recommendations on common analytical tasks. If you don't find an answer to your questions here, you might want to check our FAQ, or you can email us at support@phasegenomics.com.
This is a results manifest for the deliverable files for a custom host-finding project.
This results manifest describes the deliverables for a standard ProxiMeta project.
Phase Genomics delivers projects using sFTP servers. This document guides users through accessing their data.
The Phase Genomics platform website offers powerful capabilities to combine data from our Hi-C kits with other metagenomic data, delivering rich biological insights by leveraging the chromatin structure information of Hi-C. In addition to delivering more high-quality genomes than any other method, ProxiMeta offers the unique capability to perform host attribution for plasmids, viruses, AMR genes, and other mobile elements with no additional special experimental requirements. This page will show you how to use the Phase Genomics platform website.
Proper alignment and QC of Hi-C data is critical to getting great analytical results. Phase Genomics Hi-C kits include protocol optimizations that may make the data slightly different than what you may be used to with other Hi-C preps. Our specific recommendations for aligning, QCing, and optionally filtering data from our protocols will help you get the most out of your data.
Hi-C is a great tool for genome scaffolding, but its success depends crucially on the starting assembly. It is therefore important to ensure that your starting assembly is of sufficient quality for the scaffolding task. Our guidelines will help you make good decisions about what technologies to use and how to understand and improve scaffolding results.