Hippopotamus amphibius

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Resource Primary Assembly Alternate Assembly
GenBank mHipAmp2: GCA_030028035.1 mHipAmp2: GCA_030028045.1
ENA mHipAmp2: GCA_030028035.1 mHipAmp2: GCA_030028045.1
UCSC Genome Browser mHipAmp2: GCA_030028035.1 mHipAmp2: GCA_030028045.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mHipAmp2 1689.92 Gbp N/A 2.9 TiB
PacBio HiFi (.fq) mHipAmp2 93.73 Gbp N/A 76.8 GiB
PacBio HiFi (.bam) mHipAmp2 289.63 Gbp N/A 1.0 TiB
Arima mHipAmp2 263.82 Gbp N/A 136.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mHipAmp2 PacBio HiFi (subreads) 1689.92 Gbp N/A 2.9 TiB
PacBio HiFi (.fq) 93.73 Gbp N/A 76.8 GiB
PacBio HiFi (.bam) 289.63 Gbp N/A 1.0 TiB
Arima 263.82 Gbp N/A 136.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 June 2024.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 20 February 2023
mHipAmp2.hap1.decon.20230220.fasta.gz (721.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 96.60 Mbp 1 220.08 Mbp
20 5 81.29 Mbp 2 184.16 Mbp
30 8 71.25 Mbp 3 169.33 Mbp
40 12 61.79 Mbp 5 143.86 Mbp
50 17 46.14 Mbp 7 129.79 Mbp
60 23 35.39 Mbp 9 115.28 Mbp
70 31 28.91 Mbp 11 99.61 Mbp
80 40 24.15 Mbp 14 91.68 Mbp
90 56 10.33 Mbp 17 70.70 Mbp
100 627 16.24 Kbp 544 16.24 Kbp
1.000x 628 2.53 Gbp 545 2.53 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 20 February 2023
mHipAmp2.hap2.cur.20230220.fasta.gz (715.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 91.66 Mbp 1 231.73 Mbp
20 5 81.89 Mbp 2 199.51 Mbp
30 8 70.29 Mbp 3 188.31 Mbp
40 12 59.74 Mbp 4 174.74 Mbp
50 17 50.35 Mbp 6 149.22 Mbp
60 22 43.52 Mbp 8 144.14 Mbp
70 29 31.23 Mbp 9 137.58 Mbp
80 40 18.39 Mbp 12 104.25 Mbp
90 58 8.92 Mbp 14 80.66 Mbp
100 575 21.22 Kbp 349 21.22 Kbp
1.000x 576 2.53 Gbp 350 2.53 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/mHipAmp2.yml (view)
species: Hippopotamus amphibius
specimen: mHipAmp2
projects: 
  - vgp
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Hippopotamus_amphibius/mHipAmp2/assembly_vgp_HiC_2.0/mHipAmp2.HiC.hap1.20230116.fasta.gz
hap2: s3://genomeark/species/Hippopotamus_amphibius/mHipAmp2/assembly_vgp_HiC_2.0/mHipAmp2.HiC.hap2.20230116.fasta.gz
pretext_hap1: s3://genomeark/species/Hippopotamus_amphibius/mHipAmp2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mHipAmp2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Hippopotamus_amphibius/mHipAmp2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mHipAmp2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Hippopotamus_amphibius/mHipAmp2/assembly_vgp_HiC_2.0/evaluation/merqury/mHipAmp2_png/
pacbio_read_dir: s3://genomeark/species/Hippopotamus_amphibius/mHipAmp2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Hippopotamus_amphibius/mHipAmp2/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1+galaxy4)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of mHipAmp2, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with YAHS. The HiC prep was Arima kit 2. The kmer spectra indicates a homogametic specimen. We are submitting hap2 for curation.
Data Use Policy

Samples and data come from a variety of sources. To support fair and productive use of this data, please abide by the Data Use Policy and contact Erich D. Jarvis, ejarvis@rockefeller.edu, with any questions.