Stylephorus chordatus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fStyCho2 42.71 Gbp N/A 19.3 GiB
PacBio HiFi (.bam) fStyCho2 44.89 Gbp N/A 148.8 GiB
Arima fStyCho2 50.55 Gbp N/A 26.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 February 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fStyCho2 PacBio HiFi (.fq) 42.71 Gbp N/A 19.3 GiB
PacBio HiFi (.bam) 44.89 Gbp N/A 148.8 GiB
Arima 50.55 Gbp N/A 26.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 27 February 2025.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 25 March 2026
fStyCho2.hap1.cur.20260325.fasta.gz (312.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 27 2.84 Mbp 2 106.99 Mbp
20 75 2.08 Mbp 3 95.27 Mbp
30 140 1.53 Mbp 4 91.87 Mbp
40 230 1.13 Mbp 5 83.40 Mbp
50 353 0.82 Mbp 7 74.11 Mbp
60 519 0.61 Mbp 9 43.64 Mbp
70 755 397.41 Kbp 11 41.29 Mbp
80 1144 227.01 Kbp 14 35.57 Mbp
90 1947 91.72 Kbp 33 0.69 Mbp
100 5955 10.00 Kbp 3168 10.00 Kbp
1.000x 5955 1.17 Gbp 3168 1.17 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 25 March 2026
fStyCho2.hap2.cur.20260325.fasta.gz (303.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 28 3.22 Mbp 1 119.82 Mbp
20 74 2.05 Mbp 2 112.45 Mbp
30 140 1.46 Mbp 4 91.44 Mbp
40 229 1.11 Mbp 5 81.96 Mbp
50 348 0.85 Mbp 6 79.70 Mbp
60 507 0.61 Mbp 8 50.99 Mbp
70 729 433.73 Kbp 11 40.32 Mbp
80 1068 256.96 Kbp 14 34.99 Mbp
90 1719 115.53 Kbp 22 1.13 Mbp
100 4523 10.00 Kbp 1782 10.00 Kbp
1.000x 4523 1.14 Gbp 1782 1.14 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 29 October 2025
fStyCho2.MT.20251029.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fStyCho2.yml (view)
species: Stylephorus chordatus
specimem: fStyCho2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/assembly_vgp_HiC_2.0/fStyCho2.HiC.hap1.20251029.fasta.gz
hap2: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/assembly_vgp_HiC_2.0/fStyCho2.HiC.hap2.20251029.fasta.gz
pretext_hap1: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fStyCho2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fStyCho2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/assembly_vgp_HiC_2.0/evaluation/merqury/fStyCho2_png/
pacbio_read_dir: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Stylephorus_chordatus/fStyCho2/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.5)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.1) with mapq=10
  - VGP9 decontamination workflow (v1.1) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fStyCho2 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.