Hypomesus transpacificus

delta smelt

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


metadata.yaml (view) (edit on github)
species:
  name: Hypomesus transpacificus
  individuals:
  - short_name: fHypTra1
  short_name: fHypTra
  taxon_id: 137520
  common_name: delta smelt
  genome_size: 724000000
  genome_size_method: GoAT
  order:
    name: Osmeriformes
  family:
    name: Osmeridae
  project: [ vgp ]
Public Domain (Piqsels)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) fHypTra1 672.60 Gbp 929.01x 1.2 TiB
PacBio HiFi (.fq, Q≥20) fHypTra1 11.19 Gbp 15.45x 7.7 GiB
PacBio HiFi (.fq) fHypTra1 49.25 Gbp 68.03x 34.7 GiB
PacBio HiFi (.bam) fHypTra1 24.52 Gbp 33.87x 16.5 GiB
10x fHypTra1 130.86 Gbp 180.74x 62.9 GiB
Bionano fHypTra1 N/A 763.15x 780.3 MiB
Arima fHypTra1 154.91 Gbp 213.97x 76.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.72 Gbp.
Last upload on 6 April 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fHypTra1 PacBio HiFi (subreads) 672.60 Gbp 929.01x 1.2 TiB
PacBio HiFi (.fq, Q≥20) 11.19 Gbp 15.45x 7.7 GiB
PacBio HiFi (.fq) 49.25 Gbp 68.03x 34.7 GiB
PacBio HiFi (.bam) 24.52 Gbp 33.87x 16.5 GiB
10x 130.86 Gbp 180.74x 62.9 GiB
Bionano N/A 763.15x 780.3 MiB
Arima 154.91 Gbp 213.97x 76.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.72 Gbp.
Last upload on 6 April 2026.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 17 October 2025
fHypTra1.pri.cur.20251017.fasta.gz (137.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 15 3.16 Mbp 3 22.94 Mbp
20 48 1.39 Mbp 7 20.23 Mbp
30 127 0.69 Mbp 11 17.74 Mbp
40 274 371.59 Kbp 15 15.16 Mbp
50 549 191.76 Kbp 20 12.90 Mbp
60 1102 91.36 Kbp 27 8.32 Mbp
70 2611 22.14 Kbp 436 27.70 Kbp
80 0 0
90 0 0
100 0 0
0.709x 2972 0.51 Gbp 805 0.51 Gbp
NG based on genome size 0.72 Gbp.
Individual 1 Alternate Assembly
No assembly available.


Contigs Scaffolds
NG LG Len LG Len
10 - - - -
20 - - - -
30 - - - -
40 - - - -
50 - - - -
60 - - - -
70 - - - -
80 - - - -
90 - - - -
100 - - - -
0.000x - 0.0 Mbp - 0.0 Mbp
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 18 May 2026
fHypTra1.HiC.hap1.20260518.fasta.gz (130.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 25 1.98 Mbp 4 16.01 Mbp
20 76 1.03 Mbp 8 14.58 Mbp
30 176 0.55 Mbp 14 12.00 Mbp
40 347 332.28 Kbp 21 7.35 Mbp
50 645 183.85 Kbp 34 4.01 Mbp
60 1168 104.49 Kbp 61 1.70 Mbp
70 2175 48.93 Kbp 275 121.25 Kbp
80 0 0
90 0 0
100 0 0
0.781x 4202 0.57 Gbp 1883 0.57 Gbp
NG based on genome size 0.72 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 18 May 2026
fHypTra1.HiC.hap2.20260518.fasta.gz (116.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 25 2.02 Mbp 5 14.44 Mbp
20 87 0.80 Mbp 11 11.64 Mbp
30 215 414.15 Kbp 18 9.59 Mbp
40 456 227.63 Kbp 28 6.36 Mbp
50 902 120.80 Kbp 48 1.67 Mbp
60 1799 54.04 Kbp 201 163.15 Kbp
70 0 0
80 0 0
90 0 0
100 0 0
0.670x 3386 484.90 Mbp 1324 485.31 Mbp
NG based on genome size 0.72 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/fHypTra1.yml (view)
species: Hypomesus transpacificus
specimen: fHypTra1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_HiC_2.0/fHypTra1.HiC.hap1.20260518.fasta.gz
hap2: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_HiC_2.0/fHypTra1.HiC.hap2.20260518.fasta.gz
pretext_hap1: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fHypTra1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fHypTra1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_HiC_2.0/evaluation/merqury/fHypTra1_png/
pacbio_read_dir: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP1 genomic profiling workflow (v20260331)
  - VGP4 HiFi HiC assembly workflow (v0.6)
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10
  - VGP9 decontamination workflow (v1.3)
  - VGP6 purge-dup (v20260512)
  - Pre-curation workflow (v2.4) with mapq=10, keep HiC duplicates and generate default resolution map
notes: This was a Hifiasm-HiC assembly of fHypTra1 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.
assembly_vgp_standard_2.0/fHypTra1.yaml (view)
species: Hypomesus transpacificus
specimen: fHypTra1
projects: 
  - vgp
data_location: S3
release_to: S3
primary: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_standard_2.0/fHypTra1.standard.pri.20240515.fasta.gz
haplotigs: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_standard_2.0/fHypTra1.standard.alt.20240515.fasta.gz
pretext: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_standard_2.0/evaluation/pri/pretext/fHypTra1_pri__s2.heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/assembly_vgp_standard_2.0/evaluation/merqury/fHypTra1_png/
pacbio_read_dir: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Hypomesus_transpacificus/fHypTra1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a primary/alternate assembly of fHypTra1. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2, and the library prep kit was Swift-IDT. The HiFi k-mers were not informative for merqury, so illumina k-mers were used. 
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.