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_vgp_HiC_2.0 from 8 July 2024
mCepZeb1.HiC.hap1.20240708.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 125.21 Mbp 2 147.50 Mbp
20 6 115.75 Mbp 5 129.94 Mbp
30 9 99.44 Mbp 7 128.39 Mbp
40 13 88.32 Mbp 10 112.16 Mbp
50 17 79.49 Mbp 14 95.80 Mbp
60 22 66.50 Mbp 18 79.49 Mbp
70 29 31.29 Mbp 22 66.50 Mbp
80 50 9.41 Mbp 28 49.17 Mbp
90 118 3.05 Mbp 82 3.36 Mbp
100 792 7.59 Kbp 746 7.59 Kbp
1.000x 792 3.44 Gbp 746 3.44 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 8 July 2024
mCepZeb1.HiC.hap2.20240708.fasta.gz (1.0 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 128.30 Mbp 3 147.00 Mbp
20 8 95.17 Mbp 7 128.30 Mbp
30 13 80.11 Mbp 10 115.64 Mbp
40 18 65.90 Mbp 15 91.70 Mbp
50 26 52.63 Mbp 20 76.24 Mbp
60 36 28.76 Mbp 26 58.08 Mbp
70 64 9.60 Mbp 42 12.11 Mbp
80 134 4.51 Mbp 109 4.58 Mbp
90 280 2.04 Mbp 252 2.10 Mbp
100 942 16.40 Kbp 911 16.40 Kbp
1.000x 942 4.34 Gbp 911 4.34 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.