Dromaius novaehollandiae

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bDroNov1 72.75 Gbp N/A 32.1 GiB
Arima bDroNov1 111.82 Gbp N/A 57.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 July 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bDroNov1 PacBio HiFi (.fq) 72.75 Gbp N/A 32.1 GiB
Arima 111.82 Gbp N/A 57.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 July 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 7 January 2024
bDroNov1.hap1.cur.20240107.fasta.gz (373.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 44.90 Mbp 1 219.53 Mbp
20 7 38.96 Mbp 2 170.27 Mbp
30 10 37.44 Mbp 3 131.77 Mbp
40 15 27.06 Mbp 4 87.99 Mbp
50 21 24.24 Mbp 6 77.93 Mbp
60 28 21.09 Mbp 8 49.99 Mbp
70 37 11.59 Mbp 12 30.40 Mbp
80 52 8.25 Mbp 17 23.76 Mbp
90 77 4.09 Mbp 26 10.55 Mbp
100 400 6.03 Kbp 271 6.03 Kbp
1.000x 400 1.47 Gbp 271 1.47 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 31 August 2023
bDroNov1.hap2.cur.20230831.fasta.gz (374.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 42.39 Mbp 1 221.26 Mbp
20 6 36.73 Mbp 2 171.07 Mbp
30 10 33.96 Mbp 3 131.88 Mbp
40 15 26.96 Mbp 4 87.01 Mbp
50 20 21.06 Mbp 5 78.35 Mbp
60 27 17.96 Mbp 8 43.83 Mbp
70 36 12.47 Mbp 12 28.98 Mbp
80 50 7.41 Mbp 18 18.10 Mbp
90 80 3.10 Mbp 30 6.99 Mbp
100 339 10.77 Kbp 238 10.77 Kbp
1.000x 339 1.36 Gbp 238 1.36 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 19 July 2023
bDroNov1.MT.20230719.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bDroNov1_hap1.yml (view)
species: Dromaius novehollandiae
specimen: bDroNov1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_vgp_HiC_2.0/bDroNov1.HiC.hap1.20230719.fasta.gz
hap2: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_vgp_HiC_2.0/bDroNov1.HiC.hap2.20230719.fasta.gz
pretext_hap1: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bDroNov1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bDroNov1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_vgp_HiC_2.0/evaluation/merqury/bDroNov1_png/
mito: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_MT_rockefeller/bDroNov1.MT.20230719.fasta.gz
pacbio_read_dir: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bDroNov1, resulting in two complete haplotypes. We have confirmed metadata that this sample comes from a female bird. The k-mer spectra support this by implying a heterogametic sample, but the difference between the spectrum of each haplotype is less pronounced than it usually is for female birds. I think this is because ratites have uncharacteristically similar W and Z chromosomes, relative to other birds, according to the literature. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. 
assembly_vgp_HiC_2.0/bDroNov1_hap2.yml (view)
species: Dromaius novehollandiae
specimen: bDroNov1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_vgp_HiC_2.0/bDroNov1.HiC.hap1.20230719.fasta.gz
hap2: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_vgp_HiC_2.0/bDroNov1.HiC.hap2.20230719.fasta.gz
pretext_hap1: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bDroNov1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bDroNov1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_vgp_HiC_2.0/evaluation/merqury/bDroNov1_png/
mito: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/assembly_MT_rockefeller/bDroNov1.MT.20230719.fasta.gz
pacbio_read_dir: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Dromaius_novehollandiae/bDroNov1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bDroNov1, resulting in two complete haplotypes. We have confirmed metadata that this sample comes from a female bird. The k-mer spectra support this by implying a heterogametic sample, but the difference between the spectrum of each haplotype is less pronounced than it usually is for female birds. I think this is because ratites have uncharacteristically similar W and Z chromosomes, relative to other birds, according to the literature. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. 
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.