Ochotona princeps

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mOchPri1 278.59 Gbp N/A 615.3 GiB
PacBio HiFi (.fq) mOchPri1 83.91 Gbp N/A 62.6 GiB
PacBio HiFi (.bam) mOchPri1 70.13 Gbp N/A 240.0 GiB
Arima mOchPri1 208.38 Gbp N/A 108.5 GiB
Illumina mOchPri1 97.06 Gbp N/A 45.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 April 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mOchPri1 PacBio HiFi (subreads) 278.59 Gbp N/A 615.3 GiB
PacBio HiFi (.fq) 83.91 Gbp N/A 62.6 GiB
PacBio HiFi (.bam) 70.13 Gbp N/A 240.0 GiB
Arima 208.38 Gbp N/A 108.5 GiB
Illumina 97.06 Gbp N/A 45.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 April 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 20 June 2023
mOchPri1.hap1.cur.20230620.fasta.gz (667.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 47.79 Mbp 2 166.92 Mbp
20 11 33.86 Mbp 4 113.89 Mbp
30 20 23.41 Mbp 6 107.80 Mbp
40 33 17.26 Mbp 9 83.05 Mbp
50 51 12.19 Mbp 12 73.96 Mbp
60 77 8.10 Mbp 16 58.49 Mbp
70 118 4.83 Mbp 21 43.45 Mbp
80 205 1.89 Mbp 28 32.46 Mbp
90 869 121.15 Kbp 447 122.96 Kbp
100 6296 10.34 Kbp 5864 12.75 Kbp
1.000x 6296 2.56 Gbp 5864 2.56 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 20 June 2023
mOchPri1.hap2.cur.20230620.fasta.gz (632.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 51.07 Mbp 2 163.41 Mbp
20 10 38.30 Mbp 4 110.88 Mbp
30 19 24.09 Mbp 7 87.11 Mbp
40 31 16.76 Mbp 10 81.67 Mbp
50 50 11.31 Mbp 13 68.82 Mbp
60 77 7.35 Mbp 17 53.00 Mbp
70 129 3.34 Mbp 23 36.92 Mbp
80 305 0.61 Mbp 31 16.09 Mbp
90 1620 99.62 Kbp 1256 100.13 Kbp
100 6492 6.31 Kbp 6117 11.52 Kbp
1.000x 6492 2.53 Gbp 6117 2.53 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 February 2023
mOchPri1.MT.20230213.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mOchPri1_hap1.yml (view)
species: Ochotona princeps
specimen: mOchPri1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_vgp_HiC_2.0/mOchPri1.HiC.hap1.20230417.fasta.gz
hap2: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_vgp_HiC_2.0/mOchPri1.HiC.hap2.20230417.fasta.gz
pretext_hap1: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mOchPri1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mOchPri1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_vgp_HiC_2.0/evaluation/merqury/mOchPri1_png/
mito: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_MT_rockefeller/mOchPri1.MT.20230213.fasta.gz
pacbio_read_dir: s3://genomeark/species/Ochotona_princeps/mOchPri1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Ochotona_princeps/mOchPri1/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 mOchPri1, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with yahs. Metadata and k-mer spectra indicate a heterogametic (male) specimen. The HiC prep was Arima kit 2. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap1. 
assembly_vgp_HiC_2.0/mOchPri1_hap2.yml (view)
species: Ochotona princeps
specimen: mOchPri1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_vgp_HiC_2.0/mOchPri1.HiC.hap1.20230417.fasta.gz
hap2: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_vgp_HiC_2.0/mOchPri1.HiC.hap2.20230417.fasta.gz
pretext_hap1: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mOchPri1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mOchPri1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_vgp_HiC_2.0/evaluation/merqury/mOchPri1_png/
mito: s3://genomeark/species/Ochotona_princeps/mOchPri1/assembly_MT_rockefeller/mOchPri1.MT.20230213.fasta.gz
pacbio_read_dir: s3://genomeark/species/Ochotona_princeps/mOchPri1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Ochotona_princeps/mOchPri1/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 mOchPri1, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with yahs. Metadata and k-mer spectra indicate a heterogametic (male) specimen. The HiC prep was Arima kit 2. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap2. 
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.