Haplotype-resolved assembly of HG002 genome

We use the haplotype-resolved assembly produced by hifiasm v0.11 using 34x coverage (two 15 kb and two 20 kb libraries) by PacBio HiFi Sequel II System with Chemistry 2.0 reads (https://github.com/human-pangenomics/HG002_Data_Freeze_v1.0#hg002-data-freeze-v10-recommended-downsampled-data-mix) using kmer information from parental Illumina short reads (30× 2×150bp reads at https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=NHGRI_UCSC_panel/HG002/hpp_HG002_NA24385_son_v1/parents/ILMN/downsampled/), described recently^{2 (link)}.

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Wagner J., Olson N.D., Harris L., McDaniel J., Cheng H., Fungtammasan A., Hwang Y.C., Gupta R., Wenger A.M., Rowell W.J., Khan Z.M., Farek J., Zhu Y., Pisupati A., Mahmoud M., Xiao C., Yoo B., Sahraeian S.M., Miller D.E., Jáspez D., Lorenzo-Salazar J.M., Muñoz-Barrera A., Rubio-Rodríguez L.A., Flores C., Narzisi G., Evani U.S., Clarke W.E., Lee J., Mason C.E., Lincoln S.E., Miga K.H., Ebbert M.T., Shumate A., Li H., Chin C.S., Zook J.M, & Sedlazeck F.J. (2022). Curated variation benchmarks for challenging medically-relevant autosomal genes. Nature biotechnology, 40(5), 672-680.

Publication 2021

HiFi Sequel II System with Chemistry 2.

Freeze Haplotype Human Parents

Corresponding Organization :

Other organizations : Material Measurement Laboratory, National Institute of Standards and Technology, Dana-Farber Cancer Institute, Baylor College of Medicine, National Center for Biotechnology Information, National Institutes of Health, Children's Mercy Hospital, Seattle Children's Hospital, University of Washington, Instituto Tecnológico y de Energías Renovables, New York Genome Center, Cornell University, Invitae (United States), University of California, Santa Cruz, University of Kentucky, Johns Hopkins University

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Variable analysis

independent variables

Haplotype-resolved assembly produced by hifiasm v0.11 using 34x coverage (two 15 kb and two 20 kb libraries) by PacBio HiFi Sequel II System with Chemistry 2.0 reads
Kmer information from parental Illumina short reads (30× 2×150bp reads)

dependent variables

Not explicitly mentioned

control variables

Not explicitly mentioned

controls

No positive or negative controls are specified

Annotations

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