Tamias minimus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mTamMin1 248.44 Gbp N/A 125.7 GiB
PacBio HiFi (.bam) mTamMin1 255.06 Gbp N/A 834.4 GiB
Arima mTamMin1 224.43 Gbp N/A 120.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 December 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mTamMin1 PacBio HiFi (.fq) 248.44 Gbp N/A 125.7 GiB
PacBio HiFi (.bam) 255.06 Gbp N/A 834.4 GiB
Arima 224.43 Gbp N/A 120.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 December 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 25 March 2026
mTamMin1.HiC.hap1.20260325.fasta.gz (699.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 161.55 Mbp 2 212.35 Mbp
20 4 140.26 Mbp 3 206.34 Mbp
30 6 128.92 Mbp 4 185.52 Mbp
40 8 126.98 Mbp 6 174.52 Mbp
50 10 107.62 Mbp 7 167.22 Mbp
60 12 93.87 Mbp 9 157.09 Mbp
70 16 65.37 Mbp 11 151.95 Mbp
80 20 44.09 Mbp 13 108.26 Mbp
90 30 17.63 Mbp 15 95.64 Mbp
100 219 18.91 Kbp 138 18.91 Kbp
1.000x 219 2.65 Gbp 138 2.65 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 25 March 2026
mTamMin1.HiC.hap2.20260325.fasta.gz (657.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 182.43 Mbp 2 211.46 Mbp
20 3 181.36 Mbp 3 203.68 Mbp
30 5 138.83 Mbp 4 185.08 Mbp
40 7 128.02 Mbp 5 177.04 Mbp
50 9 116.87 Mbp 7 167.38 Mbp
60 11 89.47 Mbp 8 161.03 Mbp
70 14 83.06 Mbp 10 145.25 Mbp
80 17 59.05 Mbp 12 109.26 Mbp
90 24 16.51 Mbp 14 84.56 Mbp
100 198 14.50 Kbp 97 14.50 Kbp
1.000x 198 2.48 Gbp 97 2.48 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 25 March 2026
mTamMin1.MT.20260325.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mTamMin1.yml (view)
species: Tamias minimus
specimem: mTamMin1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Tamias_minimus/mTamMin1/assembly_vgp_HiC_2.0/mTamMin1.HiC.hap1.20260325.fasta.gz
hap2: s3://genomeark/species/Tamias_minimus/mTamMin1/assembly_vgp_HiC_2.0/mTamMin1.HiC.hap2.20260325.fasta.gz
pretext_hap1: s3://genomeark/species/Tamias_minimus/mTamMin1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mTamMin1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Tamias_minimus/mTamMin1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mTamMin1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Tamias_minimus/mTamMin1/assembly_vgp_HiC_2.0/evaluation/merqury/mTamMin1_png/
pacbio_read_dir: s3://genomeark/species/Tamias_minimus/mTamMin1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Tamias_minimus/mTamMin1/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 mTamMin1 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.