Year 2 Assembly Testing

This repo contains produced by the Human Pangenome Reference Consortium from year 2 data. Two assembly methods are tested:

• Verkko version 1.3.1
• Hifiasm version 0.19 (w/ ONT UL integration)

Assemblies for 10 year 2 samples plus HG002 are available. These assemblies are made available for internal HPRC quality control. For information about data reuse and publicating with HPRC data please see the HPRC's Data Use Protocol.

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Obtaining assemblies

Assemblies are available on our S3 bucket. The easiest way to download them is to use the URIs provided in the assembly_indexes folder of this repository. Once you have the URIs you can download the assemblies for free using the AWS CLI. For example:

aws s3 --no-sign-request cp \
	s3://human-pangenomics/submissions/53FEE631-4264-4627-8FB6-09D7364F4D3B--ASM-COMP/HG002/assemblies/verkko/HG002.verkko_filt_mat.contigs.fa.gz \
	./

Assembly File Types

For each sample, five diffent assemblies are available to download:

• hifiasm_trio_0.19_raw.txt Hifiasm trio phased assemblies
• hifiasm_hic_0.19_raw.txt Hifiasm hic phased assemblies
• verkko_trio_1.3.1_raw.txt Verkko trio phased assemblies
• verkko_gfase_1.3.1_raw.txt Verkko hic phased assemblies (GFAse)
• verkko_hic_1.3.1_raw.txt Verkko hic phased assemblies (Verkko-HiC)