Dugong dugon

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Resource Primary Assembly Alternate Assembly
GenBank mDugDug1: GCA_030020955.1 mDugDug1: GCA_030035585.1
ENA mDugDug1: GCA_030020955.1 mDugDug1: GCA_030035585.1
UCSC Genome Browser mDugDug1: GCA_030020955.1 mDugDug1: GCA_030035585.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mDugDug1 103.45 Gbp N/A 74.1 GiB
Dovetail Genomics mDugDug1 137.26 Gbp N/A 81.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 December 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mDugDug1 PacBio HiFi (.fq) 103.45 Gbp N/A 74.1 GiB
Dovetail Genomics 137.26 Gbp N/A 81.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 December 2022.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 4 February 2023
mDugDug1.hap1.cur.20230204.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 160.48 Mbp 1 211.02 Mbp
20 4 104.60 Mbp 2 198.60 Mbp
30 7 90.16 Mbp 4 196.39 Mbp
40 11 78.20 Mbp 6 177.38 Mbp
50 16 57.63 Mbp 8 140.67 Mbp
60 21 51.93 Mbp 10 130.05 Mbp
70 29 36.37 Mbp 13 115.46 Mbp
80 38 29.72 Mbp 15 102.87 Mbp
90 52 18.67 Mbp 19 79.54 Mbp
100 293 6.77 Kbp 197 6.77 Kbp
1.000x 294 3.16 Gbp 198 3.16 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 20 February 2023
mDugDug1.hap2.decon.20230220.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 160.58 Mbp 1 210.93 Mbp
20 3 139.13 Mbp 2 198.89 Mbp
30 7 81.40 Mbp 4 196.82 Mbp
40 11 70.99 Mbp 6 176.99 Mbp
50 16 57.88 Mbp 8 138.03 Mbp
60 21 49.42 Mbp 10 129.61 Mbp
70 28 37.80 Mbp 13 115.50 Mbp
80 38 28.11 Mbp 16 83.83 Mbp
90 54 16.26 Mbp 19 78.52 Mbp
100 255 7.91 Kbp 166 7.91 Kbp
1.000x 256 3.15 Gbp 167 3.15 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 21 February 2023
mDugDug1.MT.20230221.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mDugDug1.yaml (view)
species: Dugong dugon
specimen: mDugDug1
projects: 
  - vgp
hap1: s3://genomeark/species/Dugong_dugon/mDugDug1/assembly_vgp_HiC_2.0/mDugDug1.HiC.hap1.20221214.fasta.gz
hap2: s3://genomeark/species/Dugong_dugon/mDugDug1/assembly_vgp_HiC_2.0/mDugDug1.HiC.hap2.20221214.fasta.gz
pretext_hap1: s3://genomeark/species/Dugong_dugon/mDugDug1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mDugDug1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Dugong_dugon/mDugDug1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mDugDug1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Dugong_dugon/mDugDug1/assembly_vgp_HiC_2.0/evaluation/merqury/mDugDug1_png/
pacbio_read_dir: s3://genomeark/species/Dugong_dugon/mDugDug1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Dugong_dugon/mDugDug1/genomic_data/dovetail/
pipeline:
  - hifiasm (0.16.1+galaxy3)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of mDugDug1, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with YAHS. The HiC prep was Dovetail OmniC. The kmer spectra indicates a homogametic specimen. We are submitting hap1 for curation, though file locations for hap2 are included here in case it is useful. 
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.