Illex illecebrosus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) xcIllIlle1 121.94 Gbp N/A 60.8 GiB
PacBio HiFi (.bam) xcIllIlle1 130.17 Gbp N/A 431.9 GiB
Arima xcIllIlle1 212.70 Gbp N/A 110.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 May 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
xcIllIlle1 PacBio HiFi (.fq) 121.94 Gbp N/A 60.8 GiB
PacBio HiFi (.bam) 130.17 Gbp N/A 431.9 GiB
Arima 212.70 Gbp N/A 110.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 May 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 12 September 2025
xcIllIlle1.HiC.hap1.20250912.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 14 24.79 Mbp 4 105.04 Mbp
20 31 21.49 Mbp 7 98.51 Mbp
30 52 17.14 Mbp 12 89.79 Mbp
40 78 13.64 Mbp 16 87.25 Mbp
50 112 10.46 Mbp 21 80.91 Mbp
60 156 7.54 Mbp 26 74.89 Mbp
70 216 5.70 Mbp 31 70.93 Mbp
80 301 3.78 Mbp 37 67.29 Mbp
90 446 1.91 Mbp 44 51.11 Mbp
100 1550 14.80 Kbp 946 14.80 Kbp
1.000x 1550 3.96 Gbp 946 3.96 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 12 September 2025
xcIllIlle1.HiC.hap2.20250912.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 14 23.91 Mbp 4 105.16 Mbp
20 33 17.77 Mbp 8 96.37 Mbp
30 58 13.95 Mbp 12 90.47 Mbp
40 90 11.00 Mbp 17 79.37 Mbp
50 131 8.26 Mbp 22 75.80 Mbp
60 182 7.13 Mbp 27 74.66 Mbp
70 247 5.18 Mbp 32 72.48 Mbp
80 338 3.52 Mbp 38 63.46 Mbp
90 483 1.98 Mbp 45 40.09 Mbp
100 1311 14.80 Kbp 672 14.80 Kbp
1.000x 1311 3.92 Gbp 672 3.92 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 12 September 2025
xcIllIlle1.MT.20250912.fasta.gz (5.8 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/xcIllIlle1.yml (view)
species: Illex illecebrosus
specimem: xcIllIlle1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Illex_illecebrosus/xcIllIlle1/assembly_vgp_HiC_2.0/xcIllIlle1.HiC.hap1.20250912.fasta.gz
hap2: s3://genomeark/species/Illex_illecebrosus/xcIllIlle1/assembly_vgp_HiC_2.0/xcIllIlle1.HiC.hap2.20250912.fasta.gz
pretext_hap1: s3://genomeark/species/Illex_illecebrosus/xcIllIlle1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/xcIllIlle1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Illex_illecebrosus/xcIllIlle1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/xcIllIlle1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Illex_illecebrosus/xcIllIlle1/assembly_vgp_HiC_2.0/evaluation/merqury/xcIllIlle1_png/
pacbio_read_dir: s3://genomeark/species/Illex_illecebrosus/xcIllIlle1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Illex_illecebrosus/xcIllIlle1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2) using invertebrate genetic code
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.11) BUSCO mollusca_odb10
  - VGP8 HiC scaffolding workflow (v2.2) mapq set to 10, BUSCO mollusca_odb10
  - VGP9 decontamination workflow (v0.7) with database 
  - Pre-curation worklfow (v1.0beta6) mapq set to 10
notes: This was a Hifiasm-HiC assembly of xcIllIlle1 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.