Rhea pennata

lesser rhea

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank bPtePen1: GCA_028389875.1 bPtePen1: GCA_028389885.1
ENA bPtePen1: GCA_028389875.1 bPtePen1: GCA_028389885.1
UCSC Genome Browser bPtePen1: GCA_028389875.1 bPtePen1: GCA_028389885.1

metadata.yaml (view) (edit on github)
species:
  name: Rhea pennata
  individuals:
  - short_name: bPtePen1
  short_name: bPtePen
  taxon_id: 8795
  common_name: lesser rhea
  genome_size: 1645000000
  genome_size_method: GoAT
  order:
    name: Rheiformes
  family:
    name: Rheidae
  project: [ vgp ]
CC BY-SA 3.0 CHUCAO (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bPtePen1 210.95 Gbp 128.24x 489.8 GiB
PacBio HiFi (.fq) bPtePen1 54.15 Gbp 32.92x 43.7 GiB
PacBio HiFi (.bam) bPtePen1 54.17 Gbp 32.93x 187.3 GiB
Bionano bPtePen1 N/A 365.53x 1.1 GiB
Arima bPtePen1 44.48 Gbp 27.04x 22.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.65 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPtePen1 PacBio HiFi (subreads) 210.95 Gbp 128.24x 489.8 GiB
PacBio HiFi (.fq) 54.15 Gbp 32.92x 43.7 GiB
PacBio HiFi (.bam) 54.17 Gbp 32.93x 187.3 GiB
Bionano N/A 365.53x 1.1 GiB
Arima 44.48 Gbp 27.04x 22.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.65 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 17 June 2022
bPtePen1.pri.cur.20220617.fasta.gz (358.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 42.60 Mbp 0 216.94 Mbp
20 6 36.49 Mbp 1 164.82 Mbp
30 12 23.26 Mbp 2 130.21 Mbp
40 20 18.64 Mbp 4 82.47 Mbp
50 30 12.99 Mbp 7 41.21 Mbp
60 47 7.58 Mbp 13 24.52 Mbp
70 82 2.98 Mbp 23 9.40 Mbp
80 0 0
90 0 0
100 0 0
0.771x 307 1.27 Gbp 179 1.27 Gbp
NG based on genome size 1.65 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 17 June 2022
bPtePen1.alt.cur.20220617.fasta.gz (29.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 0 0
20 0 0
30 0 0
40 0 0
50 0 0
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.063x 1126 104.45 Mbp 1125 104.45 Mbp
NG based on genome size 1.65 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/bPtePen1.yaml (view)
pecies: Rhea pennata
specimen: bPtePen1
projects:
  - vgp
primary: s3://genomeark/species/Rhea_pennata/bPtePen1/assembly_vgp_standard_2.0/bPtePen1.pri.asm.20220228.fasta.gz
haplotigs: s3://genomeark/species/Rhea_pennata/bPtePen1/assembly_vgp_standard_2.0/bPtePen1.alt.asm.20220228.fasta.gz
hic_bam: s3://genomeark/species/Rhea_pennata/bPtePen1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bPtePen1_s2.bam
pretext: s3://genomeark/species/Rhea_pennata/bPtePen1/assembly_vgp_standard_2.0/evaluation/pretext/s2/bPtePen1_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Rhea_pennata/bPtePen1/assembly_vgp_standard_2.0/evaluation/merqury/p/bPtePen1_png/
pipeline:
  - hifiasm (0.16.1+galaxy2)
  - 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.