Tamiasciurus hudsonicus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mTamHud2 240.28 Gbp N/A 127.1 GiB
mTamHud3 264.16 Gbp N/A 127.8 GiB
PacBio HiFi (.bam) mTamHud2 248.98 Gbp N/A 816.2 GiB
mTamHud3 268.99 Gbp N/A 882.7 GiB
Arima mTamHud2 400.62 Gbp N/A 214.8 GiB
mTamHud3 228.46 Gbp N/A 127.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 January 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mTamHud2 PacBio HiFi (.fq) 240.28 Gbp N/A 127.1 GiB
PacBio HiFi (.bam) 248.98 Gbp N/A 816.2 GiB
Arima 400.62 Gbp N/A 214.8 GiB
mTamHud3 PacBio HiFi (.fq) 264.16 Gbp N/A 127.8 GiB
PacBio HiFi (.bam) 268.99 Gbp N/A 882.7 GiB
Arima 228.46 Gbp N/A 127.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 January 2026.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 21 April 2026
mTamHud2.hap1.cur.20260421.fasta.gz (1.5 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 148.39 Mbp 2 354.20 Mbp
20 7 129.35 Mbp 4 238.40 Mbp
30 12 98.10 Mbp 6 231.02 Mbp
40 19 71.61 Mbp 9 213.72 Mbp
50 28 50.22 Mbp 11 196.07 Mbp
60 40 37.52 Mbp 14 189.78 Mbp
70 56 26.67 Mbp 17 176.42 Mbp
80 83 14.18 Mbp 20 143.64 Mbp
90 144 5.40 Mbp 24 81.17 Mbp
100 914 8.00 Kbp 488 34.11 Kbp
1.000x 914 5.32 Gbp 488 5.32 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 21 April 2026
mTamHud2.hap2.cur.20260421.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 216.72 Mbp 2 335.71 Mbp
20 5 119.10 Mbp 4 232.66 Mbp
30 10 88.78 Mbp 6 221.29 Mbp
40 16 72.91 Mbp 8 202.12 Mbp
50 24 55.55 Mbp 10 201.01 Mbp
60 34 38.29 Mbp 13 187.77 Mbp
70 51 21.44 Mbp 15 179.87 Mbp
80 81 11.41 Mbp 18 145.75 Mbp
90 151 3.98 Mbp 22 96.87 Mbp
100 894 8.19 Kbp 426 37.22 Kbp
1.000x 894 4.80 Gbp 426 4.80 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 23 March 2026
mTamHud2.MT.20260323.fasta.gz (5.3 KiB)

Quality: not computed
Individual 3 Haplotype 1 Assembly
Version assembly_curated from 21 April 2026
mTamHud3.hap1.cur.20260421.fasta.gz (1.6 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 238.27 Mbp 2 349.19 Mbp
20 5 175.37 Mbp 4 312.19 Mbp
30 9 154.48 Mbp 6 257.74 Mbp
40 13 114.31 Mbp 8 237.73 Mbp
50 18 94.74 Mbp 10 213.34 Mbp
60 25 70.45 Mbp 13 208.05 Mbp
70 35 48.31 Mbp 16 194.93 Mbp
80 50 30.40 Mbp 19 183.41 Mbp
90 73 17.06 Mbp 22 152.57 Mbp
100 331 10.11 Kbp 140 26.22 Kbp
1.000x 331 5.72 Gbp 140 5.72 Gbp
NG based on genome size .
Individual 3 Haplotype 2 Assembly
Version assembly_curated from 21 April 2026
mTamHud3.hap2.cur.20260421.fasta.gz (1.4 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 305.15 Mbp 2 364.58 Mbp
20 5 178.80 Mbp 3 348.92 Mbp
30 8 137.39 Mbp 5 281.39 Mbp
40 12 122.52 Mbp 7 238.27 Mbp
50 17 97.18 Mbp 10 207.18 Mbp
60 23 82.56 Mbp 12 198.89 Mbp
70 31 65.25 Mbp 15 167.08 Mbp
80 41 41.32 Mbp 18 156.73 Mbp
90 60 21.01 Mbp 22 119.55 Mbp
100 290 17.75 Kbp 96 29.20 Kbp
1.000x 290 5.35 Gbp 96 5.35 Gbp
NG based on genome size .
Individual 3 Mitochondrial Assembly
Version assembly_MT_rockefeller from 25 March 2026
mTamHud3.MT.20260325.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mTamHud2.yml (view)
species: Tamiasciurus hudsonicus
specimem: mTamHud2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud2/assembly_vgp_HiC_2.0/mTamHud2.HiC.hap1.20260323.fasta.gz
hap2: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud2/assembly_vgp_HiC_2.0/mTamHud2.HiC.hap2.20260323.fasta.gz
pretext_hap1: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mTamHud2_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mTamHud2_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud2/assembly_vgp_HiC_2.0/evaluation/merqury/mTamHud2_png/
pacbio_read_dir: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud2/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.6)
  - VGP4 HiFi HiC assembly workflow (v0.5)
  - VGP8 HiC scaffolding workflow (v3.4) with mapq=10. Note that the HiC duplicates were not removed because samtools markdup tool did not have the flag -r (even if the workflow says it’s removed). 
  - VGP9 decontamination workflow (v1.3) 
  - Pre-curation worklfow (v2.2) with mapq=10, keep HiC duplicates and generate high-resolution map
notes: This was a Hifiasm-HiC assembly of mTamHud2 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.
assembly_vgp_HiC_2.0/mTamHud3.yml (view)
species: Tamiasciurus hudsonicus
specimem: mTamHud3
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud3/assembly_vgp_HiC_2.0/mTamHud3.HiC.hap1.20260325.fasta.gz
hap2: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud3/assembly_vgp_HiC_2.0/mTamHud3.HiC.hap2.20260325.fasta.gz
pretext_hap1: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mTamHud3_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mTamHud3_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud3/assembly_vgp_HiC_2.0/evaluation/merqury/mTamHud3_png/
pacbio_read_dir: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Tamiasciurus_hudsonicus/mTamHud3/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.6)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.4) with mapq=10. Note that the HiC duplicates were not removed because samtools markdup tool did not have the flag -r (even if the workflow says it’s removed). 
  - VGP9 decontamination workflow (v1.3) 
  - Pre-curation worklfow (v2.2) with mapq=10, keep HiC duplicates and generate high-resolution map
notes: This was a Hifiasm-HiC assembly of mTamHud3 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.