Toxostoma rufum

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bToxRuf1 69.81 Gbp N/A 33.3 GiB
PacBio HiFi (.bam) bToxRuf1 72.22 Gbp N/A 235.4 GiB
Arima bToxRuf1 160.77 Gbp N/A 84.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 31 October 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bToxRuf1 PacBio HiFi (.fq) 69.81 Gbp N/A 33.3 GiB
PacBio HiFi (.bam) 72.22 Gbp N/A 235.4 GiB
Arima 160.77 Gbp N/A 84.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 31 October 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 12 November 2025
bToxRuf1.HiC.hap1.20251112.fasta.gz (305.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 67.67 Mbp 1 154.70 Mbp
20 4 45.65 Mbp 2 120.33 Mbp
30 7 32.81 Mbp 3 115.93 Mbp
40 12 21.63 Mbp 5 74.81 Mbp
50 18 16.41 Mbp 6 72.88 Mbp
60 26 13.15 Mbp 8 41.86 Mbp
70 36 10.44 Mbp 12 26.09 Mbp
80 52 5.79 Mbp 17 21.63 Mbp
90 81 2.61 Mbp 24 8.31 Mbp
100 403 9.84 Kbp 220 9.84 Kbp
1.000x 403 1.18 Gbp 220 1.18 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 12 November 2025
bToxRuf1.HiC.hap2.20251112.fasta.gz (298.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 42.64 Mbp 1 154.22 Mbp
20 5 37.61 Mbp 2 121.57 Mbp
30 9 30.77 Mbp 3 116.88 Mbp
40 13 28.02 Mbp 5 74.44 Mbp
50 18 19.44 Mbp 6 74.09 Mbp
60 27 12.38 Mbp 8 40.51 Mbp
70 38 8.95 Mbp 11 31.81 Mbp
80 53 5.60 Mbp 16 21.65 Mbp
90 90 1.85 Mbp 25 7.33 Mbp
100 556 16.21 Kbp 389 16.21 Kbp
1.000x 556 1.19 Gbp 389 1.19 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 12 November 2025
bToxRuf1.MT.20251112.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bToxRuf1.yml (view)
species: Toxostoma rufum
specimem: bToxRuf1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Toxostoma_rufum/bToxRuf1/assembly_vgp_HiC_2.0/bToxRuf1.HiC.hap1.20251112.fasta.gz
hap2: s3://genomeark/species/Toxostoma_rufum/bToxRuf1/assembly_vgp_HiC_2.0/bToxRuf1.HiC.hap2.20251112.fasta.gz
pretext_hap1: s3://genomeark/species/Toxostoma_rufum/bToxRuf1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bToxRuf1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Toxostoma_rufum/bToxRuf1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bToxRuf1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Toxostoma_rufum/bToxRuf1/assembly_vgp_HiC_2.0/evaluation/merqury/bToxRuf1_png/
pacbio_read_dir: s3://genomeark/species/Toxostoma_rufum/bToxRuf1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Toxostoma_rufum/bToxRuf1/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 (v3.1) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bToxRuf1 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.