Tupaia belangeri

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mTupBel1 207.75 Gbp N/A 98.2 GiB
PacBio HiFi (.bam) mTupBel1 219.14 Gbp N/A 719.4 GiB
Arima mTupBel1 354.05 Gbp N/A 185.0 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
mTupBel1 PacBio HiFi (.fq) 207.75 Gbp N/A 98.2 GiB
PacBio HiFi (.bam) 219.14 Gbp N/A 719.4 GiB
Arima 354.05 Gbp N/A 185.0 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 10 October 2025
mTupBel1.HiC.hap1.20251010.fasta.gz (713.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 114.63 Mbp 1 341.82 Mbp
20 6 101.58 Mbp 3 195.58 Mbp
30 9 70.64 Mbp 5 139.80 Mbp
40 14 58.93 Mbp 7 126.61 Mbp
50 20 46.17 Mbp 9 120.45 Mbp
60 27 38.24 Mbp 12 107.59 Mbp
70 35 31.38 Mbp 15 72.81 Mbp
80 47 18.58 Mbp 20 60.15 Mbp
90 77 5.51 Mbp 26 34.98 Mbp
100 782 7.96 Kbp 631 7.96 Kbp
1.000x 782 3.00 Gbp 631 3.00 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 10 October 2025
mTupBel1.HiC.hap2.20251010.fasta.gz (773.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 105.62 Mbp 2 237.85 Mbp
20 7 80.65 Mbp 3 202.44 Mbp
30 12 60.48 Mbp 6 122.91 Mbp
40 18 48.56 Mbp 8 120.01 Mbp
50 26 39.65 Mbp 12 103.53 Mbp
60 36 28.55 Mbp 15 93.85 Mbp
70 49 22.26 Mbp 19 68.12 Mbp
80 70 11.78 Mbp 26 37.64 Mbp
90 115 4.39 Mbp 41 9.62 Mbp
100 987 9.60 Kbp 782 9.60 Kbp
1.000x 987 3.36 Gbp 782 3.36 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 October 2025
mTupBel1.MT.20251010.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mTupBel1.yml (view)
species: Tupaia belangeri
specimem: mTupBel1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Tupaia_belangeri/mTupBel1/assembly_vgp_HiC_2.0/mTupBel1.HiC.hap1.20251010.fasta.gz
hap2: s3://genomeark/species/Tupaia_belangeri/mTupBel1/assembly_vgp_HiC_2.0/mTupBel1.HiC.hap2.20251010.fasta.gz
pretext_hap1: s3://genomeark/species/Tupaia_belangeri/mTupBel1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mTupBel1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Tupaia_belangeri/mTupBel1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mTupBel1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Tupaia_belangeri/mTupBel1/assembly_vgp_HiC_2.0/evaluation/merqury/mTupBel1_png/
pacbio_read_dir: s3://genomeark/species/Tupaia_belangeri/mTupBel1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Tupaia_belangeri/mTupBel1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mTupBel1 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.