Forsterygion lapillum

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fForLap1 31.88 Gbp N/A 14.0 GiB
PacBio HiFi (.bam) fForLap1 32.72 Gbp N/A 102.5 GiB
Arima fForLap1 66.18 Gbp N/A 34.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 February 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fForLap1 PacBio HiFi (.fq) 31.88 Gbp N/A 14.0 GiB
PacBio HiFi (.bam) 32.72 Gbp N/A 102.5 GiB
Arima 66.18 Gbp N/A 34.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 February 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 27 August 2025
fForLap1.HiC.hap1.20250827.fasta.gz (196.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 14.29 Mbp 2 38.66 Mbp
20 14 8.09 Mbp 4 36.40 Mbp
30 25 5.79 Mbp 7 33.85 Mbp
40 43 3.64 Mbp 9 33.51 Mbp
50 70 2.23 Mbp 11 32.23 Mbp
60 127 0.97 Mbp 14 29.99 Mbp
70 246 485.04 Kbp 17 27.82 Mbp
80 526 191.87 Kbp 20 26.07 Mbp
90 1233 71.80 Kbp 25 1.49 Mbp
100 3617 5.94 Kbp 1428 5.94 Kbp
1.000x 3617 0.80 Gbp 1428 0.80 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 27 August 2025
fForLap1.HiC.hap2.20250827.fasta.gz (193.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 12.71 Mbp 3 34.94 Mbp
20 14 8.43 Mbp 5 34.50 Mbp
30 26 5.36 Mbp 7 33.76 Mbp
40 44 3.41 Mbp 9 33.09 Mbp
50 74 2.10 Mbp 12 30.71 Mbp
60 130 1.02 Mbp 15 29.16 Mbp
70 242 478.55 Kbp 17 27.73 Mbp
80 492 211.94 Kbp 20 26.18 Mbp
90 1088 83.69 Kbp 24 15.45 Mbp
100 3104 6.31 Kbp 1009 6.31 Kbp
1.000x 3104 0.78 Gbp 1009 0.79 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 27 August 2025
fForLap1.MT.20250827.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fForLap1.yml (view)
species: Forsterygion lapillum
specimem: fForLap1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Forsterygion_lapillum/fForLap1/assembly_vgp_HiC_2.0/fForLap1.HiC.hap1.20250827.fasta.gz
hap2: s3://genomeark/species/Forsterygion_lapillum/fForLap1/assembly_vgp_HiC_2.0/fForLap1.HiC.hap2.20250827.fasta.gz
pretext_hap1: s3://genomeark/species/Forsterygion_lapillum/fForLap1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fForLap1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Forsterygion_lapillum/fForLap1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fForLap1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Forsterygion_lapillum/fForLap1/assembly_vgp_HiC_2.0/evaluation/merqury/fForLap1_png/
pacbio_read_dir: s3://genomeark/species/Forsterygion_lapillum/fForLap1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Forsterygion_lapillum/fForLap1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.1)
  - VGP1 genomic profiling workflow (v0.3)
  - VGP4 HiFi HiC assembly workflow (v0.3.9)
  - VGP8 HiC scaffolding workflow (v2.0)
  - VGP9 decontamination workflow (v0.7) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm-HiC assembly of fForLap1 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.