Lycodopsis pacificus

blackbelly eelpout

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


Resource Primary Assembly Alternate Assembly
GenBank fLycPai1: GCA_028021495.1 fLycPai1: GCA_028022725.1
ENA fLycPai1: GCA_028021495.1 fLycPai1: GCA_028022725.1
UCSC Genome Browser fLycPai1: GCA_028021495.1 fLycPai1: GCA_028022725.1

metadata.yaml (view) (edit on github)
species:
  common_name: blackbelly eelpout
  name: Lycodopsis pacificus
  short_name: fLycPai
  taxon_id: 1772091
  order:
    name: Scorpaeniformes
  family:
    name: Zoarcidae
  individuals:
  - short_name: fLycPai1
  genome_size: 649712992
  genome_size_method: 
  project: [ ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fa) fLycPai1 17.14 Gbp 26.39x 5.5 GiB
PacBio HiFi (.fq) fLycPai1 25.96 Gbp 39.95x 21.4 GiB
Arima fLycPai1 414.64 Gbp 638.19x 200.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.65 Gbp.
Last upload on 26 January 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fLycPai1 PacBio HiFi (.fa) 17.14 Gbp 26.39x 5.5 GiB
PacBio HiFi (.fq) 25.96 Gbp 39.95x 21.4 GiB
Arima 414.64 Gbp 638.19x 200.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.65 Gbp.
Last upload on 26 January 2023.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 16 December 2022
fLycPai1.pri.cur.20221216.fasta.gz (180.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 13.24 Mbp 1 32.99 Mbp
20 10 10.56 Mbp 3 31.51 Mbp
30 16 7.90 Mbp 6 29.72 Mbp
40 26 6.08 Mbp 8 29.06 Mbp
50 38 4.72 Mbp 10 27.72 Mbp
60 54 3.44 Mbp 12 26.74 Mbp
70 77 2.43 Mbp 15 24.76 Mbp
80 111 1.47 Mbp 18 23.04 Mbp
90 175 0.66 Mbp 21 20.35 Mbp
100 0 0
0.995x 475 0.65 Gbp 109 0.65 Gbp
NG based on genome size 0.65 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 16 December 2022
fLycPai1.alt.cur.20221216.fasta.gz (0.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 0 0
20 0 0
30 0 0
40 0 0
50 0 0
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.005x 52 3.35 Mbp 52 3.35 Mbp
NG based on genome size 0.65 Gbp.
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 8 October 2022
fLycPac1.HiC.hap1.20221008.fasta.gz (182.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 11.87 Mbp 1 33.37 Mbp
20 10 9.74 Mbp 3 30.64 Mbp
30 18 7.12 Mbp 6 29.19 Mbp
40 28 5.79 Mbp 8 28.84 Mbp
50 41 4.67 Mbp 10 28.11 Mbp
60 57 3.52 Mbp 13 25.54 Mbp
70 82 2.03 Mbp 15 24.85 Mbp
80 121 1.28 Mbp 18 23.35 Mbp
90 191 0.67 Mbp 21 19.90 Mbp
100 523 52.39 Kbp 154 55.74 Kbp
1.013x 782 0.66 Gbp 409 0.66 Gbp
NG based on genome size 0.65 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 8 October 2022
fLycPac1.HiC.hap2.20221008.fasta.gz (181.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 13.24 Mbp 1 32.89 Mbp
20 10 10.56 Mbp 3 31.37 Mbp
30 16 7.90 Mbp 6 29.18 Mbp
40 26 6.08 Mbp 8 29.06 Mbp
50 38 4.72 Mbp 10 27.52 Mbp
60 54 3.44 Mbp 13 25.58 Mbp
70 77 2.43 Mbp 15 24.72 Mbp
80 111 1.47 Mbp 18 22.39 Mbp
90 174 0.69 Mbp 21 20.35 Mbp
100 0 179 1.00 Kbp
1.000x 523 0.65 Gbp 180 0.65 Gbp
NG based on genome size 0.65 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/fLycPai1_hap2.yaml (view)
species: Lycodopsis pacificus
specimen: fLycPai1
projects: 
  - vgp
hap2: s3://genomeark/species/Lycodopsis_pacificus/fLycPac1/assembly_vgp_HiC_2.0/fLycPac1.HiC.hap2.20221008.fasta.gz
pretext_hap2: s3://genomeark/species/Lycodopsis_pacificus/fLycPac1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fLycPac1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Lycodopsis_pacificus/fLycPac1/assembly_vgp_HiC_2.0/evaluation/fLycPac1_png/
pacbio_read_dir: s3://genomeark/species/Lycodopsis_pacificus/fLycPac1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Lycodopsis_pacificus/fLycPac1/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1+galaxy2)
  - yahs (1.2a+galaxy1)
assembled_by_group: Rockefeller
notes: This was a Hifiasm-HiC assembly of fLycPai1 (VGL-fLycPac1), which produced phased hap1 and hap2 assemblies. Both haplotypes are uploaded to genomeark, but Please curate hap2 ( fLycPac1.HiC.hap2.20221008.fasta.gz ), as it looks like the more complete assembly between the two of them. This individual did not have bionano data. Scaffolding was done with YAHS. Merqury spectra plots of contigs indicate a homogametic specimen. 
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.