Axis porcinus

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


No image
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_curated from 21 January 2026
mAxiPor1.hap1.cur.20260121.fasta.gz (778.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 96.23 Mbp 2 132.09 Mbp
20 6 88.88 Mbp 5 111.74 Mbp
30 10 63.96 Mbp 7 100.65 Mbp
40 14 62.88 Mbp 10 90.72 Mbp
50 19 54.16 Mbp 13 81.78 Mbp
60 24 49.31 Mbp 17 69.18 Mbp
70 30 42.93 Mbp 21 63.48 Mbp
80 37 37.23 Mbp 26 57.72 Mbp
90 51 8.85 Mbp 31 47.34 Mbp
100 1173 13.57 Kbp 719 14.63 Kbp
1.000x 1173 2.77 Gbp 719 2.77 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 21 January 2026
mAxiPor1.hap2.cur.20260121.fasta.gz (667.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 96.31 Mbp 3 116.90 Mbp
20 6 87.06 Mbp 5 100.78 Mbp
30 9 82.30 Mbp 8 93.22 Mbp
40 13 69.15 Mbp 11 84.45 Mbp
50 18 52.30 Mbp 14 78.41 Mbp
60 23 50.23 Mbp 18 64.76 Mbp
70 28 46.78 Mbp 23 55.34 Mbp
80 35 34.33 Mbp 28 50.70 Mbp
90 118 0.63 Mbp 34 30.48 Mbp
100 3330 504 bp 1968 12.60 Kbp
1.000x 3330 2.72 Gbp 1968 2.72 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.