Urocitellus parryii

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mUroPar1 139.53 Gbp N/A 73.0 GiB
PacBio HiFi (.bam) mUroPar1 139.77 Gbp N/A 565.7 GiB
Arima mUroPar1 485.66 Gbp N/A 257.7 GiB
mUroPar3 203.90 Gbp N/A 107.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 April 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mUroPar1 PacBio HiFi (.fq) 139.53 Gbp N/A 73.0 GiB
PacBio HiFi (.bam) 139.77 Gbp N/A 565.7 GiB
Arima 485.66 Gbp N/A 257.7 GiB
mUroPar3 Arima 203.90 Gbp N/A 107.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 April 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 30 September 2024
mUroPar1.hap1.cur.20240930.fasta.gz (822.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 68.41 Mbp 2 226.67 Mbp
20 9 52.56 Mbp 3 220.21 Mbp
30 15 44.23 Mbp 4 211.85 Mbp
40 23 33.83 Mbp 6 199.38 Mbp
50 33 23.16 Mbp 7 184.16 Mbp
60 51 13.03 Mbp 9 146.46 Mbp
70 82 6.97 Mbp 11 131.43 Mbp
80 143 3.23 Mbp 14 71.74 Mbp
90 304 0.97 Mbp 19 13.30 Mbp
100 3223 1.79 Kbp 2529 10.40 Kbp
1.000x 3223 2.94 Gbp 2529 2.94 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 30 September 2024
mUroPar1.hap2.cur.20240930.fasta.gz (766.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 55.72 Mbp 1 284.05 Mbp
20 9 49.32 Mbp 3 199.36 Mbp
30 16 39.20 Mbp 4 198.10 Mbp
40 24 28.33 Mbp 5 197.89 Mbp
50 35 19.27 Mbp 7 168.11 Mbp
60 53 11.43 Mbp 9 143.43 Mbp
70 85 6.58 Mbp 11 134.65 Mbp
80 146 3.02 Mbp 13 72.50 Mbp
90 323 0.78 Mbp 37 3.02 Mbp
100 2897 913 bp 2307 17.36 Kbp
1.000x 2897 2.75 Gbp 2307 2.75 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 July 2024
mUroPar1.MT.20240717.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mUroPar1.yml (view)
species: Urocitellus parryii
specimen: mUroPar1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Urocitellus_parryii/mUroPar1/assembly_vgp_HiC_2.0/mUroPar1.HiC.hap1.20240517.fasta.gz
hap2: s3://genomeark/species/Urocitellus_parryii/mUroPar1/assembly_vgp_HiC_2.0/mUroPar1.HiC.hap2.20240517.fasta.gz
pretext_hap1: s3://genomeark/species/Urocitellus_parryii/mUroPar1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mUroPar1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Urocitellus_parryii/mUroPar1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mUroPar1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Urocitellus_parryii/mUroPar1/assembly_vgp_HiC_2.0/evaluation/merqury/hap1_purged/mUroPar1_png/
mito: s3://genomeark/species/Urocitellus_parryii/mUroPar1/assembly_MT_rockefeller/mUroPar1.MT.20240717.fasta.gz
pacbio_read_dir: s3://genomeark/species/Urocitellus_parryii/mUroPar1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Urocitellus_parryii/mUroPar1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mUroPar1, resulting in two complete haplotypes. The HiC prep kit used was Arima, so the HiC reads require trimming 5 bp off the 5' end. The assembly was performed on the Rockefeller University VGL instance. 
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.