Pseudorca crassidens

false killer whale

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Pseudorca crassidens
  individuals:
  - short_name: mPseCra1
  short_name: mPseCra
  taxon_id: 82174
  common_name: false killer whale
  genome_size: 3081000000
  genome_size_method: GoAT
  order:
    name: Artiodactyla
  family:
    name: Delphinidae
  project: [ vgp ]
CC BY 2.0 NOAA/NMFS/PIFSC by Jim Cotton (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mPseCra1 382.18 Gbp 124.04x 0.9 TiB
PacBio HiFi (.fq) mPseCra1 116.44 Gbp 37.79x 93.8 GiB
PacBio HiFi (.bam) mPseCra1 116.99 Gbp 37.97x 403.2 GiB
Bionano mPseCra1 N/A 270.84x 1.7 GiB
Dovetail Genomics mPseCra1 480.40 Gbp 155.92x 245.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.08 Gbp.
Last upload on 7 August 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPseCra1 PacBio HiFi (subreads) 382.18 Gbp 124.04x 0.9 TiB
PacBio HiFi (.fq) 116.44 Gbp 37.79x 93.8 GiB
PacBio HiFi (.bam) 116.99 Gbp 37.97x 403.2 GiB
Bionano N/A 270.84x 1.7 GiB
Dovetail Genomics 480.40 Gbp 155.92x 245.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.08 Gbp.
Last upload on 7 August 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 29 April 2024
mPseCra1.hap1.cur.20240429.fa.gz (653.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 149.43 Mbp 2 186.66 Mbp
20 5 92.04 Mbp 4 155.77 Mbp
30 9 80.72 Mbp 6 136.06 Mbp
40 13 62.00 Mbp 8 116.59 Mbp
50 19 49.41 Mbp 11 108.01 Mbp
60 27 33.15 Mbp 14 92.81 Mbp
70 38 24.14 Mbp 18 86.16 Mbp
80 68 4.10 Mbp 22 38.63 Mbp
90 0 0
100 0 0
0.867x 561 2.67 Gbp 438 2.67 Gbp
NG based on genome size 3.08 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 29 April 2024
mPseCra1.hap2.cur.20240429.fa.gz (620.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 110.51 Mbp 2 198.34 Mbp
20 6 104.79 Mbp 4 151.83 Mbp
30 9 91.99 Mbp 6 134.42 Mbp
40 13 60.87 Mbp 8 110.51 Mbp
50 18 44.58 Mbp 11 105.74 Mbp
60 27 31.46 Mbp 14 91.47 Mbp
70 38 19.96 Mbp 18 82.42 Mbp
80 92 2.27 Mbp 33 5.27 Mbp
90 0 0
100 0 0
0.861x 549 2.65 Gbp 416 2.68 Gbp
NG based on genome size 3.08 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 8 May 2024
mPseCra1.MT.20240508.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mPseCra1.yml (view)
species: Pseudorca crassidens
specimen: mPseCra1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Pseudorca_crassidens/mPseCra1/assembly_vgp_HiC_2.0/mPseCra1.HiC.hap1.20240226.fasta.gz
hap2: s3://genomeark/species/Pseudorca_crassidens/mPseCra1/assembly_vgp_HiC_2.0/mPseCra1.HiC.hap2.20240226.fasta.gz
pretext_hap1: s3://genomeark/species/Pseudorca_crassidens/mPseCra1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mPseCra1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Pseudorca_crassidens/mPseCra1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mPseCra1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Pseudorca_crassidens/mPseCra1/assembly_vgp_HiC_2.0/evaluation/merqury/mPseCra1_png/
pacbio_read_dir: s3://genomeark/species/Pseudorca_crassidens/mPseCra1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Pseudorca_crassidens/mPseCra1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Pseudorca_crassidens/mPseCra1/genomic_data/dovetail/
mito: s3://genomeark/species/Pseudorca_crassidens/mPseCra1/assembly_MT_rockefeller/mPseCra1.MT.20240508.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - solve (3.7)
  - yahs (1.2a.1)
notes: This was a Hifiasm-HiC assembly of mPseCra1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Dovetail OmniC.
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.