Thorius spilogaster

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aThoSpi2 949.54 Gbp N/A 466.5 GiB
PacBio HiFi (.bam) aThoSpi2 988.39 Gbp N/A 3.1 TiB
Arima aThoSpi2 1426.89 Gbp N/A 758.2 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
aThoSpi2 PacBio HiFi (.fq) 949.54 Gbp N/A 466.5 GiB
PacBio HiFi (.bam) 988.39 Gbp N/A 3.1 TiB
Arima 1426.89 Gbp N/A 758.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 31 October 2025.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 23 June 2026
aThoSpi2.HiC.hap1.20260623.fasta.gz (6.5 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
1 8.42 Gbp
1 8.42 Gbp
1 8.42 Gbp
2 4.41 Gbp
3 4.33 Gbp
3 4.33 Gbp
4 3.45 Gbp
5 2.29 Gbp
6 1.33 Gbp
6228 4.24 Kbp
6228 26.07 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 23 June 2026
aThoSpi2.HiC.hap2.20260623.fasta.gz (6.4 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 19 108.17 Mbp 1 7.71 Gbp
20 49 76.23 Mbp 1 7.71 Gbp
30 87 60.74 Mbp 2 2.86 Gbp
40 135 48.63 Mbp 2 2.86 Gbp
50 193 40.04 Mbp 4 2.23 Gbp
60 266 32.05 Mbp 5 2.14 Gbp
70 359 23.81 Mbp 6 2.08 Gbp
80 489 16.56 Mbp 7 1.67 Gbp
90 698 8.71 Mbp 9 1.17 Gbp
100 4124 12.47 Kbp 2895 12.47 Kbp
1.000x 4124 25.92 Gbp 2895 25.92 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 23 June 2026
aThoSpi2.MT.20260623.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/aThoSpi2.yml (view)
species: Thorius spilogaster
specimen: aThoSpi2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Thorius_spilogaster/aThoSpi2/assembly_vgp_HiC_2.0/aThoSpi2.HiC.hap1.20260623.fasta.gz
hap2: s3://genomeark/species/Thorius_spilogaster/aThoSpi2/assembly_vgp_HiC_2.0/aThoSpi2.HiC.hap2.20260623.fasta.gz
pretext_hap1: s3://genomeark/species/Thorius_spilogaster/aThoSpi2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/aThoSpi2_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Thorius_spilogaster/aThoSpi2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/aThoSpi2_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Thorius_spilogaster/aThoSpi2/assembly_vgp_HiC_2.0/evaluation/merqury/aThoSpi2_png/
pacbio_read_dir: s3://genomeark/species/Thorius_spilogaster/aThoSpi2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Thorius_spilogaster/aThoSpi2/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 (v3.5) with mapq=10. Note that the scaffolding steps completed but the QC steps failed, because of the largest scaffolds were >2.1Gbp in size. The largest scaffolds were manually broken into smaller parts. Compleasm was run on the split fasta. 
  - VGP9 decontamination workflow (v1.3). Note that the decontamination workflow was ran on the fasta with the largest scaffolds (>2.1Gbp) being split into smaller parts. 
  - Pre-curation workflow (v20260526 update) with mapq=10, keep HiC duplicates and generate ultra-high resolution map. Note that the workflow failed at the step of of combining the HiFi bam files (samtools merge) for the coverage track. Hence, the coverage track and the coverage gap track were added manually to pretextmap in local HPC. 
notes: This was a Hifiasm-HiC assembly of aThoSpi2 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.