Tamias striatus

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


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mTamStr1 195.19 Gbp N/A 99.1 GiB
PacBio HiFi (.bam) mTamStr1 199.12 Gbp N/A 659.7 GiB
Arima mTamStr1 351.46 Gbp N/A 189.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mTamStr1 PacBio HiFi (.fq) 195.19 Gbp N/A 99.1 GiB
PacBio HiFi (.bam) 199.12 Gbp N/A 659.7 GiB
Arima 351.46 Gbp N/A 189.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 3 November 2025
mTamStr1.HiC.hap1.20251103.fasta.gz (684.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 165.58 Mbp 1 361.34 Mbp
20 4 145.08 Mbp 2 224.95 Mbp
30 6 118.47 Mbp 3 207.59 Mbp
40 8 102.76 Mbp 5 179.69 Mbp
50 11 84.39 Mbp 6 173.24 Mbp
60 14 63.48 Mbp 8 162.33 Mbp
70 19 45.81 Mbp 9 145.29 Mbp
80 27 19.36 Mbp 11 144.40 Mbp
90 52 5.03 Mbp 14 81.93 Mbp
100 504 17.86 Kbp 352 17.86 Kbp
1.000x 504 2.58 Gbp 352 2.58 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 3 November 2025
mTamStr1.HiC.hap2.20251103.fasta.gz (745.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 172.03 Mbp 1 405.64 Mbp
20 4 156.71 Mbp 2 229.29 Mbp
30 6 144.08 Mbp 3 216.56 Mbp
40 8 119.00 Mbp 5 175.70 Mbp
50 10 101.72 Mbp 7 170.09 Mbp
60 13 84.56 Mbp 8 159.77 Mbp
70 18 49.64 Mbp 10 149.35 Mbp
80 25 30.03 Mbp 12 139.11 Mbp
90 44 7.76 Mbp 15 88.95 Mbp
100 366 23.61 Kbp 255 23.61 Kbp
1.000x 366 2.81 Gbp 255 2.81 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 3 November 2025
mTamStr1.MT.20251103.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mTamStr1.yml (view)
species: Tamias striatus
specimem: mTamStr1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Tamias_striatus/mTamStr1/assembly_vgp_HiC_2.0/mTamStr1.HiC.hap1.20251103.fasta.gz
hap2: s3://genomeark/species/Tamias_striatus/mTamStr1/assembly_vgp_HiC_2.0/mTamStr1.HiC.hap2.20251103.fasta.gz
pretext_hap1: s3://genomeark/species/Tamias_striatus/mTamStr1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mTamStr1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Tamias_striatus/mTamStr1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mTamStr1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Tamias_striatus/mTamStr1/assembly_vgp_HiC_2.0/evaluation/merqury/mTamStr1_png/
pacbio_read_dir: s3://genomeark/species/Tamias_striatus/mTamStr1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Tamias_striatus/mTamStr1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v3.1) with mapq=10
  - VGP9 decontamination workflow (v1.0)
  - VGP6 purge dups (v0.10.4) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mTamStr1 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. A haplotig track (in the format of a coverage track) was injected to pretextmap for hap1, based on the 2-copy k-mers in hap1 assembly at the raw read coverage of <100x.
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.