Rucervus eldii

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


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mRucEld1 132.51 Gbp N/A 57.8 GiB
PacBio HiFi (.bam) mRucEld1 135.69 Gbp N/A 441.2 GiB
Arima mRucEld1 156.61 Gbp N/A 85.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 April 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mRucEld1 PacBio HiFi (.fq) 132.51 Gbp N/A 57.8 GiB
PacBio HiFi (.bam) 135.69 Gbp N/A 441.2 GiB
Arima 156.61 Gbp N/A 85.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 April 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 12 January 2026
mRucEld1.hap1.cur.20260112.fasta.gz (824.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 101.85 Mbp 3 157.79 Mbp
20 8 78.66 Mbp 5 134.64 Mbp
30 13 61.97 Mbp 8 118.49 Mbp
40 19 55.61 Mbp 12 86.22 Mbp
50 26 49.83 Mbp 16 78.23 Mbp
60 34 41.37 Mbp 21 62.31 Mbp
70 52 7.53 Mbp 28 49.08 Mbp
80 323 0.78 Mbp 153 1.15 Mbp
90 1060 318.96 Kbp 692 415.91 Kbp
100 4373 7.59 Kbp 3421 7.59 Kbp
1.000x 4373 3.65 Gbp 3421 3.65 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 12 January 2026
mRucEld1.hap2.cur.20260112.fasta.gz (693.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 100.50 Mbp 2 155.45 Mbp
20 6 82.85 Mbp 4 145.90 Mbp
30 10 68.04 Mbp 6 123.52 Mbp
40 14 61.65 Mbp 9 115.07 Mbp
50 19 55.29 Mbp 11 94.15 Mbp
60 24 51.22 Mbp 14 81.07 Mbp
70 30 44.43 Mbp 18 69.21 Mbp
80 37 30.82 Mbp 23 52.40 Mbp
90 55 6.73 Mbp 28 44.43 Mbp
100 1299 6.94 Kbp 902 6.94 Kbp
1.000x 1299 2.79 Gbp 902 2.79 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 27 May 2025
mRucEld1.MT.20250527.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mRucEld1.yml (view)
species: Rucervus eldii
specimem: mRucEld1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Rucervus_eldii/mRucEld1/assembly_vgp_HiC_2.0/mRucEld1.HiC.hap1.20250602.fasta.gz
hap2: s3://genomeark/species/Rucervus_eldii/mRucEld1/assembly_vgp_HiC_2.0/mRucEld1.HiC.hap2.20250602.fasta.gz
pretext_hap1: s3://genomeark/species/Rucervus_eldii/mRucEld1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mRucEld1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Rucervus_eldii/mRucEld1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mRucEld1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Rucervus_eldii/mRucEld1/assembly_vgp_HiC_2.0/evaluation/merqury/mRucEld1_png/
pacbio_read_dir: s3://genomeark/species/Rucervus_eldii/mRucEld1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Rucervus_eldii/mRucEld1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2)
  - VGP1 genomic profiling workflow (v0.1.8)
  - VGP4 HiFi HiC assembly workflow (v0.3.6)
  - VGP8 HiC scaffolding workflow (v1.8), re-run compleasm with correct input for hap2
  - VGP9 decontamination workflow (v0.6) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta5)
notes: This was a Hifiasm-HiC assembly of mRucEld1 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.