From Assembly to chromosome bins

mdozmorov / HiC_tools

A collection of tools for Hi-C data analysis

MIT License

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Closed mictadlo closed 5 years ago

mictadlo commented 5 years ago

Hi, We have a denovo plant genome assembly and HiC data but without any annotation. We would like to get 19 chromosome bins (19 FASTA files).

Which tool could work for us?

Thank you in advance,

Michal

mdozmorov commented 5 years ago

De novo genome scaffolding using Hi-C is the area I'm least familiar with. Hope others will comment. In a meantime, can recommend papers from Phase Genomics company, they specialize in genome scaffolding: https://phasegenomics.com/publications/#papers. They also have a software FAQ, https://phasegenomics.com/resources/#faq_software, and a documentation with recommendations on scaffolding, https://phasegenomics.github.io/

mdozmorov commented 5 years ago

More tools for de novo genome assembly from Hi-C reads: https://omictools.com/assembly-scaffolding-1-category