Eschrichtius robustus

grey whale

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


Resource Primary Assembly Alternate Assembly
GenBank mEscRob2: GCA_028021215.1 mEscRob2: GCA_028021475.1
ENA mEscRob2: GCA_028021215.1 mEscRob2: GCA_028021475.1
UCSC Genome Browser mEscRob2: GCA_028021215.1 mEscRob2: GCA_028021475.1

metadata.yaml (view) (edit on github)
species:
  short_name: mEscRob
  name: Eschrichtius robustus
  taxon_id: 9764
  common_name: grey whale
  order:
    name: Artiodactyla
  family:
    name: Eschrichtiidae
  individuals:
    - short_name: mEscRob1
      provider: Marlys Houck, Phillip Morin
      sex: male
  genome_size: 2870000000
  genome_size_method: GoaT ancestral inferred
  project: [ vgp ]
CC BY-SA 2.0 Gregory "Slobirdr" Smith (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mEscRob2 278.91 Gbp 97.18x 657.1 GiB
PacBio HiFi (.fq) mEscRob2 84.99 Gbp 29.61x 64.4 GiB
Bionano mEscRob1 N/A 263.83x 1.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.87 Gbp.
Last upload on 1 August 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mEscRob1 Bionano N/A 263.83x 1.1 GiB
mEscRob2 PacBio HiFi (subreads) 278.91 Gbp 97.18x 657.1 GiB
PacBio HiFi (.fq) 84.99 Gbp 29.61x 64.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.87 Gbp.
Last upload on 1 August 2024.
Assemblies
Individual 2 Primary Assembly
Version assembly_curated from 1 December 2022
mEscRob2.pri.cur.20221201.fasta.gz (759.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 106.74 Mbp 1 190.21 Mbp
20 5 88.75 Mbp 3 152.77 Mbp
30 8 77.16 Mbp 4 147.58 Mbp
40 12 66.95 Mbp 6 139.74 Mbp
50 18 40.98 Mbp 9 126.54 Mbp
60 26 29.73 Mbp 11 114.12 Mbp
70 37 22.16 Mbp 14 100.89 Mbp
80 55 11.39 Mbp 17 86.87 Mbp
90 126 2.09 Mbp 20 67.02 Mbp
100 406 0.51 Mbp 164 0.71 Mbp
1.039x 982 2.98 Gbp 703 2.98 Gbp
NG based on genome size 2.87 Gbp.
Individual 2 Alternate Assembly
Version assembly_curated from 1 December 2022
mEscRob2.alt.cur.20221201.fasta.gz (719.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 133 1.58 Mbp 133 1.58 Mbp
20 351 1.11 Mbp 351 1.11 Mbp
30 650 0.84 Mbp 650 0.84 Mbp
40 1033 0.67 Mbp 1033 0.67 Mbp
50 1524 0.52 Mbp 1524 0.52 Mbp
60 2161 390.56 Kbp 2161 390.56 Kbp
70 3050 267.60 Kbp 3050 267.60 Kbp
80 4432 156.52 Kbp 4432 156.52 Kbp
90 7568 52.68 Kbp 7568 52.68 Kbp
100 0 0
0.971x 14442 2.79 Gbp 14442 2.79 Gbp
NG based on genome size 2.87 Gbp.
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 21 November 2022
mEscRob2.MT.20221121.fasta.gz (4.9 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/mEscRob2.yaml (view)
species: Eschrichtius robustus
specimen: mEscRob2
projects:
  - vgp
primary: s3://genomeark/species/Eschrichtius_robustus/mEscRob2/assembly_vgp_standard_2.0/mEscRob2.standard.pri.20221005.fasta.gz
pretext: s3://genomeark/species/Eschrichtius_robustus/mEscRob2/assembly_vgp_standard_2.0/evaluation/pretext/mEscRob2_hap2__s2_heatmap.pretext
haplotigs: s3://genomeark/species/Eschrichtius_robustus/mEscRob2/assembly_vgp_standard_2.0/intermediates/mEscRob2_c2.fasta.gz
kmer_spectra_img: s3://genomeark/species/Eschrichtius_robustus/mEscRob2/assembly_vgp_standard_2.0/evaluation/merqury/mEscRob2_png
pacbio_read_dir: s3://genomeark/species/Eschrichtius_robustus/mEscRob2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: SRR12437598
pipeline:
  - hifiasm (0.16.1+galaxy3)
  - yahs (1.2a+galaxy1)
assembled_by_group: Rockefeller
notes: This assembly was run with the standard hifiasm pipeline (ie, pseudohaplotype) with hifiasm internal purging set at intermediate. There was no bionano data. Hi-C reads were generated from a different indvidual than the HiFi reads. For Hi-C reads we put the SRR accession number as they were from DNAzoo. 
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.