Psilogobius mainlandi

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fPsiMai1 117.93 Gbp N/A 52.7 GiB
PacBio HiFi (.bam) fPsiMai1 120.50 Gbp N/A 391.6 GiB
Arima fPsiMai1 106.17 Gbp N/A 55.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fPsiMai1 PacBio HiFi (.fq) 117.93 Gbp N/A 52.7 GiB
PacBio HiFi (.bam) 120.50 Gbp N/A 391.6 GiB
Arima 106.17 Gbp N/A 55.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 June 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 1 July 2026
fPsiMai1.hap1.cur.20260701.fasta.gz (380.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 55.74 Mbp 3 63.22 Mbp
20 6 46.87 Mbp 5 62.90 Mbp
30 9 42.58 Mbp 7 62.26 Mbp
40 12 34.99 Mbp 9 62.03 Mbp
50 17 27.48 Mbp 12 59.33 Mbp
60 23 20.09 Mbp 14 57.22 Mbp
70 31 15.78 Mbp 16 54.84 Mbp
80 41 11.57 Mbp 19 46.93 Mbp
90 56 6.22 Mbp 22 40.05 Mbp
100 333 13.49 Kbp 253 13.49 Kbp
1.000x 333 1.39 Gbp 253 1.39 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 1 July 2026
fPsiMai1.hap2.cur.20260701.fasta.gz (350.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 47.92 Mbp 3 62.75 Mbp
20 6 45.93 Mbp 5 62.21 Mbp
30 9 42.18 Mbp 7 61.59 Mbp
40 13 32.90 Mbp 9 61.08 Mbp
50 17 24.51 Mbp 11 59.14 Mbp
60 23 20.81 Mbp 14 56.88 Mbp
70 30 17.77 Mbp 16 54.76 Mbp
80 39 13.20 Mbp 19 45.79 Mbp
90 53 6.90 Mbp 22 36.60 Mbp
100 236 12.92 Kbp 154 12.92 Kbp
1.000x 236 1.36 Gbp 154 1.36 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 12 September 2025
fPsiMai1.MT.20250912.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fPsiMai1.yml (view)
species: Psilogobius mainlandi
specimem: fPsiMai1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/assembly_vgp_HiC_2.0/fPsiMai1.HiC.hap1.20250925.fasta.gz
hap2: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/assembly_vgp_HiC_2.0/fPsiMai1.HiC.hap2.20250925.fasta.gz
pretext_hap1: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fPsiMai1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fPsiMai1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/assembly_vgp_HiC_2.0/evaluation/merqury/fPsiMai1_png/
pacbio_read_dir: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Psilogobius_mainlandi/fPsiMai1/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 (v0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fPsiMai1 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.