Cephalophus zebra

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mCepZeb1 140.42 Gbp N/A 71.5 GiB
PacBio HiFi (.bam) mCepZeb1 142.44 Gbp N/A 576.3 GiB
Arima mCepZeb1 277.67 Gbp N/A 147.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mCepZeb1 PacBio HiFi (.fq) 140.42 Gbp N/A 71.5 GiB
PacBio HiFi (.bam) 142.44 Gbp N/A 576.3 GiB
Arima 277.67 Gbp N/A 147.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 20 October 2025
mCepZeb1.hap1.cur.20251020.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 128.59 Mbp 2 250.11 Mbp
20 7 104.19 Mbp 4 164.26 Mbp
30 11 91.70 Mbp 6 146.48 Mbp
40 16 76.24 Mbp 9 134.06 Mbp
50 21 65.81 Mbp 12 117.25 Mbp
60 28 49.96 Mbp 16 110.63 Mbp
70 39 20.35 Mbp 20 87.93 Mbp
80 75 6.79 Mbp 25 77.35 Mbp
90 163 3.12 Mbp 32 9.42 Mbp
100 783 7.59 Kbp 598 7.59 Kbp
1.000x 783 3.92 Gbp 598 3.92 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 20 October 2025
mCepZeb1.hap2.cur.20251020.fasta.gz (830.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 125.21 Mbp 2 220.76 Mbp
20 7 102.72 Mbp 5 141.37 Mbp
30 11 89.00 Mbp 7 133.65 Mbp
40 15 82.26 Mbp 10 123.29 Mbp
50 20 66.39 Mbp 14 103.58 Mbp
60 28 38.45 Mbp 18 89.57 Mbp
70 46 12.62 Mbp 22 73.03 Mbp
80 102 4.64 Mbp 28 60.48 Mbp
90 238 1.88 Mbp 102 2.24 Mbp
100 839 22.26 Kbp 677 22.26 Kbp
1.000x 839 3.84 Gbp 677 3.84 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/mCepZeb1.yml (view)
species: Cephalophus zebra
specimen: mCepZeb1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Cephalophus_zebra/mCepZeb1/assembly_vgp_HiC_2.0/mCepZeb1.HiC.hap1.20240708.fasta.gz
hap2: s3://genomeark/species/Cephalophus_zebra/mCepZeb1/assembly_vgp_HiC_2.0/mCepZeb1.HiC.hap2.20240708.fasta.gz
pretext_hap1: s3://genomeark/species/Cephalophus_zebra/mCepZeb1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mCepZeb1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Cephalophus_zebra/mCepZeb1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mCepZeb1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Cephalophus_zebra/mCepZeb1/assembly_vgp_HiC_2.0/evaluation/merqury/mCepZeb1_png/
pacbio_read_dir: s3://genomeark/species/Cephalophus_zebra/mCepZeb1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Cephalophus_zebra/mCepZeb1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy1)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mCepZeb1, 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.