Contopus sordidulus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bConSor1 67.50 Gbp N/A 30.2 GiB
PacBio HiFi (.bam) bConSor1 69.61 Gbp N/A 217.7 GiB
Arima bConSor1 83.05 Gbp N/A 43.7 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
bConSor1 PacBio HiFi (.fq) 67.50 Gbp N/A 30.2 GiB
PacBio HiFi (.bam) 69.61 Gbp N/A 217.7 GiB
Arima 83.05 Gbp N/A 43.7 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 6 October 2025
bConSor1.HiC.hap1.20251006.fasta.gz (279.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 37.58 Mbp 1 118.20 Mbp
20 6 24.63 Mbp 2 116.58 Mbp
30 11 19.78 Mbp 3 97.27 Mbp
40 17 16.15 Mbp 5 74.14 Mbp
50 24 13.34 Mbp 6 67.00 Mbp
60 32 11.27 Mbp 8 55.74 Mbp
70 44 8.62 Mbp 10 36.84 Mbp
80 58 6.30 Mbp 14 21.59 Mbp
90 81 3.18 Mbp 19 19.35 Mbp
100 415 10.67 Kbp 197 10.67 Kbp
1.000x 415 1.06 Gbp 197 1.06 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 October 2025
bConSor1.HiC.hap2.20251006.fasta.gz (290.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 39.47 Mbp 1 117.70 Mbp
20 7 22.47 Mbp 2 116.54 Mbp
30 12 19.56 Mbp 3 97.65 Mbp
40 19 14.42 Mbp 5 74.91 Mbp
50 27 12.82 Mbp 6 74.23 Mbp
60 36 11.39 Mbp 8 64.91 Mbp
70 46 8.95 Mbp 10 39.64 Mbp
80 62 5.40 Mbp 13 35.75 Mbp
90 88 3.11 Mbp 17 21.52 Mbp
100 302 8.73 Kbp 106 8.73 Kbp
1.000x 302 1.09 Gbp 106 1.09 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 October 2025
bConSor1.MT.20251006.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bConSor1.yml (view)
species: Contopus sordidulus
specimem: bConSor1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Contopus_sordidulus/bConSor1/assembly_vgp_HiC_2.0/bConSor1.HiC.hap1.20251006.fasta.gz
hap2: s3://genomeark/species/Contopus_sordidulus/bConSor1/assembly_vgp_HiC_2.0/bConSor1.HiC.hap2.20251006.fasta.gz
pretext_hap1: s3://genomeark/species/Contopus_sordidulus/bConSor1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bConSor1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Contopus_sordidulus/bConSor1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bConSor1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Contopus_sordidulus/bConSor1/assembly_vgp_HiC_2.0/evaluation/merqury/bConSor1_png/
pacbio_read_dir: s3://genomeark/species/Contopus_sordidulus/bConSor1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Contopus_sordidulus/bConSor1/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 bConSor1 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.