Opisthocomus hoazin

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bOpiHoa1 1145.38 Gbp N/A 1.9 TiB
PacBio HiFi (.fq) bOpiHoa1 56.50 Gbp N/A 44.2 GiB
PacBio HiFi (.bam) bOpiHoa1 176.15 Gbp N/A 611.5 GiB
Arima bOpiHoa1 121.26 Gbp N/A 59.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bOpiHoa1 PacBio HiFi (subreads) 1145.38 Gbp N/A 1.9 TiB
PacBio HiFi (.fq) 56.50 Gbp N/A 44.2 GiB
PacBio HiFi (.bam) 176.15 Gbp N/A 611.5 GiB
Arima 121.26 Gbp N/A 59.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 3 August 2023
bOpiHoa1.hap1.cur.20230803.fasta.gz (397.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 40.42 Mbp 1 157.52 Mbp
20 8 26.46 Mbp 3 109.48 Mbp
30 14 21.99 Mbp 4 96.05 Mbp
40 21 18.59 Mbp 6 88.57 Mbp
50 30 14.27 Mbp 7 80.95 Mbp
60 43 9.35 Mbp 9 75.34 Mbp
70 62 6.30 Mbp 13 30.29 Mbp
80 90 4.30 Mbp 18 22.22 Mbp
90 138 2.17 Mbp 26 12.43 Mbp
100 683 14.50 Kbp 415 14.50 Kbp
1.000x 683 1.48 Gbp 415 1.48 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 3 August 2023
bOpiHoa1.hap2.cur.20230803.fasta.gz (358.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 33.48 Mbp 1 156.93 Mbp
20 9 25.59 Mbp 2 133.21 Mbp
30 14 22.33 Mbp 4 96.35 Mbp
40 21 18.74 Mbp 5 88.44 Mbp
50 30 13.96 Mbp 7 75.69 Mbp
60 40 11.16 Mbp 8 74.87 Mbp
70 55 7.66 Mbp 12 30.14 Mbp
80 77 4.60 Mbp 18 19.43 Mbp
90 120 2.07 Mbp 27 9.91 Mbp
100 535 15.49 Kbp 323 15.49 Kbp
1.000x 535 1.36 Gbp 323 1.36 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 29 August 2023
bOpiHoa1.MT.20230829.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bOpiHoa1_hap1.yml (view)
species: Opisthocomus hoazin
specimen: bOpiHoa1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/assembly_vgp_HiC_2.0/bOpiHoa1.HiC.hap1.20230227.fasta.gz
hap2: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/assembly_vgp_HiC_2.0/bOpiHoa1.HiC.hap2.20230227.fasta.gz
pretext_hap1: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bOpiHoa1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bOpiHoa1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/assembly_vgp_HiC_2.0/evaluation/merqury/bOpiHoa1_png/
mito: s3://genomeark/working/temp_mitos/bOpiHoa1_mitohifi_final.fasta.gz
pacbio_read_dir: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1+galaxy4)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bOpiHoa1, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The kmer spectra indicates a heterogametic specimen, so we are submitting both haplotypes as tickets, in case the sex chromosomes need to be fished out between the haplotypes. This is the curation ticket for hap1. MitoHiFi was run on the raw reads, and the resulting mitogenome is included in this ticket for help with mitochondrial decontam, but the final mitogenome we upload may differ as we want to verify the presence of a large repeat in the mito assembly.
assembly_vgp_HiC_2.0/bOpiHoa1_hap2.yml (view)
species: Opisthocomus hoazin
specimen: bOpiHoa1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/assembly_vgp_HiC_2.0/bOpiHoa1.HiC.hap1.20230227.fasta.gz
hap2: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/assembly_vgp_HiC_2.0/bOpiHoa1.HiC.hap2.20230227.fasta.gz
pretext_hap1: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bOpiHoa1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bOpiHoa1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/assembly_vgp_HiC_2.0/evaluation/merqury/bOpiHoa1_png/
mito: s3://genomeark/working/temp_mitos/bOpiHoa1_mitohifi_final.fasta.gz
pacbio_read_dir: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Opisthocomus_hoazin/bOpiHoa1/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1+galaxy4)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bOpiHoa1, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The kmer spectra indicates a heterogametic specimen, so we are submitting both haplotypes as tickets, in case the sex chromosomes need to be fished out between the haplotypes. This is the curation ticket for hap2. MitoHiFi was run on the raw reads, and the resulting mitogenome is included in this ticket for help with mitochondrial decontam, but the final mitogenome we upload may differ as we want to verify the presence of a large repeat in the mito assembly.
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.