Tamias amoenus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mTamAmo1 207.34 Gbp N/A 92.7 GiB
PacBio HiFi (.bam) mTamAmo1 211.20 Gbp N/A 690.9 GiB
Arima mTamAmo1 180.46 Gbp N/A 97.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 November 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mTamAmo1 PacBio HiFi (.fq) 207.34 Gbp N/A 92.7 GiB
PacBio HiFi (.bam) 211.20 Gbp N/A 690.9 GiB
Arima 180.46 Gbp N/A 97.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 November 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 23 January 2026
mTamAmo1.HiC.hap1.20260123.fasta.gz (728.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 167.54 Mbp 1 0.55 Gbp
20 4 156.00 Mbp 2 263.53 Mbp
30 6 143.28 Mbp 3 259.74 Mbp
40 8 138.77 Mbp 4 208.42 Mbp
50 10 102.51 Mbp 5 188.29 Mbp
60 13 69.07 Mbp 7 171.28 Mbp
70 18 48.51 Mbp 8 163.19 Mbp
80 25 24.31 Mbp 10 147.71 Mbp
90 43 8.06 Mbp 12 84.73 Mbp
100 476 16.33 Kbp 280 16.33 Kbp
1.000x 476 2.77 Gbp 280 2.77 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 23 January 2026
mTamAmo1.HiC.hap2.20260123.fasta.gz (676.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 164.33 Mbp 1 0.61 Gbp
20 4 127.94 Mbp 1 0.61 Gbp
30 6 124.93 Mbp 2 346.61 Mbp
40 8 115.07 Mbp 3 303.72 Mbp
50 10 90.01 Mbp 4 292.86 Mbp
60 13 83.83 Mbp 4 292.86 Mbp
70 18 42.96 Mbp 6 155.09 Mbp
80 27 16.96 Mbp 7 153.34 Mbp
90 48 7.71 Mbp 9 135.41 Mbp
100 388 14.24 Kbp 159 14.24 Kbp
1.000x 388 2.55 Gbp 159 2.55 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 23 January 2026
mTamAmo1.MT.20260123.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mTamAmo1.yml (view)
species: Tamias amoenus
specimem: mTamAmo1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Tamias_amoenus/mTamAmo1/assembly_vgp_HiC_2.0/mTamAmo1.HiC.hap1.20260123.fasta.gz
hap2: s3://genomeark/species/Tamias_amoenus/mTamAmo1/assembly_vgp_HiC_2.0/mTamAmo1.HiC.hap2.20260123.fasta.gz
pretext_hap1: s3://genomeark/species/Tamias_amoenus/mTamAmo1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mTamAmo1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Tamias_amoenus/mTamAmo1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mTamAmo1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Tamias_amoenus/mTamAmo1/assembly_vgp_HiC_2.0/evaluation/merqury/mTamAmo1_png/
pacbio_read_dir: s3://genomeark/species/Tamias_amoenus/mTamAmo1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Tamias_amoenus/mTamAmo1/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 (v3.2) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - VGP6 purge-dups workflow (v0.10.4)
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mTamAmo1 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.