Osmerus mordax

rainbow smelt

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Osmerus mordax
  individuals:
  - short_name: fOsmMor3
  short_name: fOsmMor
  taxon_id: 8014
  common_name: rainbow smelt
  genome_size: 675000000
  genome_size_method: GoAT
  order:
    name: Osmeriformes
  family:
    name: Osmeridae
  project: [ vgp ]
CC BY-SA 2.0 NOAA Great Lakes Environmental Research Laboratory (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) fOsmMor3 238.11 Gbp 352.76x 485.2 GiB
PacBio HiFi (.fq) fOsmMor3 24.80 Gbp 36.74x 20.6 GiB
PacBio HiFi (.bam) fOsmMor3 24.76 Gbp 36.67x 86.7 GiB
Bionano fOsmMor3 N/A 482.13x 388.6 MiB
Arima fOsmMor3 119.58 Gbp 177.15x 56.7 GiB
Illumina fOsmMor3 49.37 Gbp 73.13x 23.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.68 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fOsmMor3 PacBio HiFi (subreads) 238.11 Gbp 352.76x 485.2 GiB
PacBio HiFi (.fq) 24.80 Gbp 36.74x 20.6 GiB
PacBio HiFi (.bam) 24.76 Gbp 36.67x 86.7 GiB
Bionano N/A 482.13x 388.6 MiB
Arima 119.58 Gbp 177.15x 56.7 GiB
Illumina 49.37 Gbp 73.13x 23.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.68 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 3 Primary Assembly
Version assembly_curated from 16 January 2024
fOsmMor3.pri.cur.20240116.fasta.gz (136.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 11 4.94 Mbp 3 23.87 Mbp
20 36 1.74 Mbp 6 21.97 Mbp
30 93 0.90 Mbp 9 19.32 Mbp
40 195 0.52 Mbp 13 18.31 Mbp
50 371 282.89 Kbp 17 16.63 Mbp
60 705 146.17 Kbp 21 14.02 Mbp
70 1484 50.26 Kbp 27 10.68 Mbp
80 0 0
90 0 0
100 0 0
0.737x 2272 497.31 Mbp 365 497.67 Mbp
NG based on genome size 0.68 Gbp.
Individual 3 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
Assembly Metadata
assembly_vgp_standard_2.0/fOsmMor3.yml (view)
species: Osmerus mordax
specimen: fOsmMor3
projects: 
  - vgp
data_location: S3
release_to: S3
primary: s3://genomeark/species/Osmerus_mordax/fOsmMor3/assembly_vgp_standard_2.0/fOsmMor3.standard.pri.20231017.fasta.gz
haplotigs: s3://genomeark/species/Osmerus_mordax/fOsmMor3/assembly_vgp_standard_2.0/fOsmMor3.standard.alt.20231017.fasta.gz
pretext: s3://genomeark/species/Osmerus_mordax/fOsmMor3/assembly_vgp_standard_2.0/evaluation/pri/pretext/fOsmMor3_pri__s2.heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Osmerus_mordax/fOsmMor3/assembly_vgp_standard_2.0/evaluation/merqury/fOsmMor3_png/
pacbio_read_dir: s3://genomeark/species/Osmerus_mordax/fOsmMor3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Osmerus_mordax/fOsmMor3/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Osmerus_mordax/fOsmMor3/genomic_data/bionano/
pipeline:
  - hifiasm (0.18.8-r525)
  - solve (3.7)
  - yahs (1.2a.1)
assembled_by_group: Rockefeller
notes: This was a primary/alternate assembly of fOsmMor3. This individual had bionano data. HiC scaffolding was performed with yahs. The HiC prep was Swift-IDT.
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.