Amblysomus hottentotus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mAmbHot1 232.63 Gbp N/A 105.5 GiB
PacBio HiFi (.bam) mAmbHot1 242.95 Gbp N/A 796.4 GiB
Arima mAmbHot1 786.81 Gbp N/A 410.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 November 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mAmbHot1 PacBio HiFi (.fq) 232.63 Gbp N/A 105.5 GiB
PacBio HiFi (.bam) 242.95 Gbp N/A 796.4 GiB
Arima 786.81 Gbp N/A 410.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 November 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 January 2026
mAmbHot1.HiC.hap1.20260106.fasta.gz (1.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 161.96 Mbp 2 315.44 Mbp
20 8 147.79 Mbp 5 211.31 Mbp
30 13 107.82 Mbp 8 153.06 Mbp
40 19 78.41 Mbp 13 122.88 Mbp
50 29 59.46 Mbp 19 96.33 Mbp
60 40 46.41 Mbp 27 64.68 Mbp
70 64 17.83 Mbp 38 37.96 Mbp
80 129 5.18 Mbp 69 12.14 Mbp
90 415 1.07 Mbp 214 1.69 Mbp
100 2996 13.37 Kbp 2599 13.37 Kbp
1.000x 2996 6.26 Gbp 2599 6.26 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 January 2026
mAmbHot1.HiC.hap2.20260106.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 215.76 Mbp 1 0.57 Gbp
20 5 174.70 Mbp 2 0.54 Gbp
30 8 130.20 Mbp 4 265.94 Mbp
40 13 99.93 Mbp 6 245.11 Mbp
50 18 87.69 Mbp 9 112.54 Mbp
60 25 68.21 Mbp 14 98.97 Mbp
70 34 41.69 Mbp 20 59.45 Mbp
80 53 16.61 Mbp 30 33.73 Mbp
90 147 2.39 Mbp 76 4.52 Mbp
100 1448 13.59 Kbp 1114 13.59 Kbp
1.000x 1448 5.06 Gbp 1114 5.06 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 16 May 2025
mAmbHot1.MT.20250516.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mAmbHot1.yml (view)
species: Amblysomus hottentotus
specimem: mAmbHot1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: no curation
hap1: s3://genomeark/species/Amblysomus_hottentotus/mAmbHot1/assembly_vgp_HiC_2.0/mAmbHot1.HiC.hap1.20260106.fasta.gz
hap2: s3://genomeark/species/Amblysomus_hottentotus/mAmbHot1/assembly_vgp_HiC_2.0/mAmbHot1.HiC.hap2.20260106.fasta.gz
pretext_hap1: s3://genomeark/species/Amblysomus_hottentotus/mAmbHot1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mAmbHot1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Amblysomus_hottentotus/mAmbHot1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mAmbHot1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Amblysomus_hottentotus/mAmbHot1/assembly_vgp_HiC_2.0/evaluation/merqury/mAmbHot1_png/
pacbio_read_dir: s3://genomeark/species/Amblysomus_hottentotus/mAmbHot1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Amblysomus_hottentotus/mAmbHot1/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 (v3.2) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mAmbHot1 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. The HiC signals are too faint for manual curation.
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.