Rhynochetos jubatus

kagu

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bRhyJub1: GCA_027574665.1 bRhyJub1: GCA_027595965.1
ENA bRhyJub1: GCA_027574665.1 bRhyJub1: GCA_027595965.1
UCSC Genome Browser bRhyJub1: GCA_027574665.1 bRhyJub1: GCA_027595965.1

metadata.yaml (view) (edit on github)
species:
  name: Rhynochetos jubatus
  individuals:
  - short_name: bRhyJub1
  short_name: bRhyJub
  taxon_id: 54386
  common_name: kagu
  genome_size: 1424000000
  genome_size_method: GoAT
  order:
    name: Gruiformes
  family:
    name: Rhynochetidae
  project: [ vgp ]
CC BY-SA 3.0 Quartl (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bRhyJub1 328.62 Gbp 230.77x 698.0 GiB
PacBio HiFi (.fq) bRhyJub1 50.86 Gbp 35.71x 39.2 GiB
PacBio HiFi (.bam) bRhyJub1 50.59 Gbp 35.53x 173.4 GiB
Bionano bRhyJub1 N/A 527.55x 1.4 GiB
Arima bRhyJub1 83.61 Gbp 58.72x 43.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.42 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bRhyJub1 PacBio HiFi (subreads) 328.62 Gbp 230.77x 698.0 GiB
PacBio HiFi (.fq) 50.86 Gbp 35.71x 39.2 GiB
PacBio HiFi (.bam) 50.59 Gbp 35.53x 173.4 GiB
Bionano N/A 527.55x 1.4 GiB
Arima 83.61 Gbp 58.72x 43.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.42 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 16 June 2022
bRhyJub1.pri.cur.20220616.fasta.gz (356.6 MiB)

Quality: 0.3 errors/Mb (QV=64.99)

Contigs Scaffolds
NG LG Len LG Len
10 4 26.37 Mbp 0 148.63 Mbp
20 10 23.31 Mbp 2 126.03 Mbp
30 17 16.80 Mbp 3 85.19 Mbp
40 27 13.33 Mbp 4 79.19 Mbp
50 39 9.65 Mbp 6 63.59 Mbp
60 56 7.10 Mbp 10 31.64 Mbp
70 84 4.06 Mbp 16 22.07 Mbp
80 130 2.24 Mbp 24 13.33 Mbp
90 229 0.82 Mbp 52 2.05 Mbp
100 0 0
0.935x 448 1.33 Gbp 148 1.33 Gbp
NG based on genome size 1.42 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 16 June 2022
bRhyJub1.alt.cur.20220616.fasta.gz (215.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 55 1.85 Mbp 55 1.85 Mbp
20 155 1.16 Mbp 155 1.16 Mbp
30 309 0.75 Mbp 309 0.75 Mbp
40 553 453.03 Kbp 553 453.03 Kbp
50 1096 127.91 Kbp 1096 127.91 Kbp
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.556x 2819 0.79 Gbp 2818 0.79 Gbp
NG based on genome size 1.42 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/bRhyJub1.yaml (view)
species: Rhynochetos jubatus
specimen: bRhyJub1
projects:
  - vgp
primary: s3://genomeark/species/Rhynochetos_jubatus/bRhyJub1/assembly_vgp_standard_2.0/bRhyJub1.pri.asm.20220317.fasta.gz
haplotigs: s3://genomeark/species/Rhynochetos_jubatus/bRhyJub1/assembly_vgp_standard_2.0/bRhyJub1.alt.asm.20220317.fasta.gz
hic_bam: s3://genomeark/species/Rhynochetos_jubatus/bRhyJub1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bRhyJub1_s2.bam
pretext: s3://genomeark/species/Rhynochetos_jubatus/bRhyJub1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bRhyJub1_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Rhynochetos_jubatus/bRhyJub1/assembly_vgp_standard_2.0/evaluation/merqury/p/bRhyJub1_png/
pipeline:
  - hifiasm (0.16.1+galaxy2)
  - purge_dups (1.2.5+galaxy4)
  - 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.