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_vgp_HiC_2.0 from 2 June 2025
mRucEld1.HiC.hap1.20250602.fasta.gz (717.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 101.85 Mbp 2 256.48 Mbp
20 8 82.35 Mbp 3 232.52 Mbp
30 13 67.59 Mbp 5 157.79 Mbp
40 19 59.68 Mbp 8 119.79 Mbp
50 25 52.50 Mbp 12 83.69 Mbp
60 33 42.50 Mbp 17 71.74 Mbp
70 50 7.56 Mbp 23 41.06 Mbp
80 321 0.78 Mbp 154 1.15 Mbp
90 1057 318.83 Kbp 696 414.68 Kbp
100 4407 7.59 Kbp 3457 7.59 Kbp
1.000x 4407 3.65 Gbp 3457 3.65 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 2 June 2025
mRucEld1.HiC.hap2.20250602.fasta.gz (693.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 100.50 Mbp 1 322.25 Mbp
20 6 82.85 Mbp 3 162.09 Mbp
30 10 68.04 Mbp 5 145.35 Mbp
40 14 61.65 Mbp 7 117.34 Mbp
50 19 55.56 Mbp 9 102.52 Mbp
60 24 52.40 Mbp 12 84.33 Mbp
70 30 44.43 Mbp 16 75.14 Mbp
80 36 38.12 Mbp 20 61.13 Mbp
90 53 7.25 Mbp 26 41.02 Mbp
100 1304 6.94 Kbp 917 6.94 Kbp
1.000x 1304 2.79 Gbp 917 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.