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
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 October 2021.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fHypTra1 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 October 2021.
Assemblies

No assemblies.

Assembly Metadata
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.