Axis porcinus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mAxiPor1 124.86 Gbp N/A 57.0 GiB
PacBio HiFi (.bam) mAxiPor1 127.79 Gbp N/A 415.0 GiB
Arima mAxiPor1 205.66 Gbp N/A 112.4 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
mAxiPor1 PacBio HiFi (.fq) 124.86 Gbp N/A 57.0 GiB
PacBio HiFi (.bam) 127.79 Gbp N/A 415.0 GiB
Arima 205.66 Gbp N/A 112.4 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 21 May 2025
mAxiPor1.HiC.hap1.20250521.fasta.gz (655.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 95.36 Mbp 2 203.32 Mbp
20 6 88.40 Mbp 3 154.09 Mbp
30 9 76.61 Mbp 5 132.09 Mbp
40 13 63.37 Mbp 7 96.94 Mbp
50 17 61.56 Mbp 10 87.66 Mbp
60 21 52.29 Mbp 13 77.78 Mbp
70 26 49.97 Mbp 16 63.48 Mbp
80 32 40.87 Mbp 20 59.21 Mbp
90 40 15.89 Mbp 25 44.60 Mbp
100 1155 14.63 Kbp 885 14.63 Kbp
1.000x 1155 2.51 Gbp 885 2.51 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 21 May 2025
mAxiPor1.HiC.hap2.20250521.fasta.gz (726.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 100.18 Mbp 3 132.05 Mbp
20 7 86.76 Mbp 5 117.30 Mbp
30 10 70.95 Mbp 8 103.54 Mbp
40 15 63.20 Mbp 11 95.76 Mbp
50 20 52.20 Mbp 14 85.52 Mbp
60 26 47.97 Mbp 18 69.15 Mbp
70 33 41.32 Mbp 23 60.74 Mbp
80 41 21.83 Mbp 28 49.69 Mbp
90 152 0.61 Mbp 39 7.58 Mbp
100 3614 12.60 Kbp 2049 12.60 Kbp
1.000x 3614 2.99 Gbp 2049 2.99 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 12 May 2025
mAxiPor1.MT.20250512.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mAxiPor1.yml (view)
species: Axis porcinus
specimem: mAxiPor1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Axis_porcinus/mAxiPor1/assembly_vgp_HiC_2.0/mAxiPor1.HiC.hap1.20250521.fasta.gz
hap2: s3://genomeark/species/Axis_porcinus/mAxiPor1/assembly_vgp_HiC_2.0/mAxiPor1.HiC.hap2.20250521.fasta.gz
pretext_hap1: s3://genomeark/species/Axis_porcinus/mAxiPor1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mAxiPor1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Axis_porcinus/mAxiPor1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mAxiPor1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Axis_porcinus/mAxiPor1/assembly_vgp_HiC_2.0/evaluation/merqury/mAxiPor1_png/
pacbio_read_dir: s3://genomeark/species/Axis_porcinus/mAxiPor1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Axis_porcinus/mAxiPor1/genomic_data/arima/
pipeline:
  - hifiasm (0.24.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
notes: This was a Hifiasm-HiC assembly of mAxiPor1 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.