Spheniscus humboldti

Humboldt's penguin

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bSphHub1: GCA_027474245.1 bSphHub1: GCA_027474345.1
ENA bSphHub1: GCA_027474245.1 bSphHub1: GCA_027474345.1
UCSC Genome Browser bSphHub1: GCA_027474245.1 bSphHub1: GCA_027474345.1

metadata.yaml (view) (edit on github)
species:
  name: Spheniscus humboldti
  individuals:
  - short_name: bSphHub1
  short_name: bSphHub
  taxon_id: '9240'
  common_name: Humboldt's penguin
  genome_size: 1594000000
  genome_size_method: GoAT
  order:
    name: Sphenisciformes
  family:
    name: Spheniscidae
  project: [ vgp ]
CC BY-SA 2.0 Frank_am_Main (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bSphHub1 268.64 Gbp 168.53x 575.9 GiB
PacBio HiFi (.fq) bSphHub1 44.85 Gbp 28.14x 35.2 GiB
PacBio HiFi (.bam) bSphHub1 44.70 Gbp 28.04x 153.8 GiB
Bionano bSphHub1 N/A 887.53x 2.5 GiB
Arima bSphHub1 93.66 Gbp 58.76x 48.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.59 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bSphHub1 PacBio HiFi (subreads) 268.64 Gbp 168.53x 575.9 GiB
PacBio HiFi (.fq) 44.85 Gbp 28.14x 35.2 GiB
PacBio HiFi (.bam) 44.70 Gbp 28.04x 153.8 GiB
Bionano N/A 887.53x 2.5 GiB
Arima 93.66 Gbp 58.76x 48.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.59 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 22 March 2022
bSphHub1.pri.cur.20220322.fasta.gz (381.9 MiB)

Quality: 0.5 errors/Mb (QV=63.40)

Contigs Scaffolds
NG LG Len LG Len
10 3 31.53 Mbp 0 231.54 Mbp
20 9 21.91 Mbp 1 180.14 Mbp
30 17 19.15 Mbp 2 136.02 Mbp
40 26 15.34 Mbp 3 92.12 Mbp
50 39 11.03 Mbp 5 84.17 Mbp
60 56 8.10 Mbp 7 76.04 Mbp
70 84 4.67 Mbp 12 25.83 Mbp
80 141 1.43 Mbp 22 9.20 Mbp
90 0 0
100 0 0
0.852x 389 1.36 Gbp 136 1.36 Gbp
NG based on genome size 1.59 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 22 March 2022
bSphHub1.alt.cur.20220322.fasta.gz (328.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 95 1.22 Mbp 95 1.22 Mbp
20 252 0.86 Mbp 252 0.86 Mbp
30 467 0.64 Mbp 467 0.64 Mbp
40 755 478.12 Kbp 755 478.12 Kbp
50 1144 352.30 Kbp 1144 352.30 Kbp
60 1718 212.60 Kbp 1718 212.60 Kbp
70 3023 53.99 Kbp 3023 53.99 Kbp
80 0 0
90 0 0
100 0 0
0.728x 4343 1.16 Gbp 4342 1.16 Gbp
NG based on genome size 1.59 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/bSphHub1.yaml (view)
species: Spheniscus humboldti
specimen: bSphHub1
projects:
  - vgp
primary: s3://genomeark/species/Spheniscus_humboldti/bSphHub1/assembly_vgp_standard_2.0/bSphHub1.pri.asm.20220209.fasta.gz
haplotigs: s3://genomeark/species/Spheniscus_humboldti/bSphHub1/assembly_vgp_standard_2.0/bSphHub1.alt.asm.20220209.fasta.gz
hic_bam: s3://genomeark/species/Spheniscus_humboldti/bSphHub1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bSphHub1_s2.bam
pretext: s3://genomeark/species/Spheniscus_humboldti/bSphHub1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bSphHub1_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Spheniscus_humboldti/bSphHub1/assembly_vgp_standard_2.0/evaluation/merqury/p/bSphHub1_png/
pipeline:
  - hifiasm (0.16.1+galaxy1)
  - purge_dups (1.2.5+galaxy3)
  - solve (3.7.0+galaxy0)
  - salsa (2.3+galaxy2)
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.