Sebastes fasciatus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fSebFas1 40.35 Gbp 48.40x 18.1 GiB
PacBio HiFi (.bam) fSebFas1 376.49 Gbp 451.52x 168.4 GiB
Arima fSebFas4 86.16 Gbp 103.33x 45.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.83 Gbp.
Last upload on 21 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fSebFas1 PacBio HiFi (.fq) 40.35 Gbp 48.40x 18.1 GiB
PacBio HiFi (.bam) 376.49 Gbp 451.52x 168.4 GiB
fSebFas4 Arima 86.16 Gbp 103.33x 45.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.83 Gbp.
Last upload on 21 March 2024.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 26 July 2024
fSebFas1.pri.cur.20240726.fasta.gz (215.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 23.37 Mbp 2 43.64 Mbp
20 8 14.70 Mbp 4 40.69 Mbp
30 15 11.63 Mbp 6 38.53 Mbp
40 23 9.83 Mbp 9 36.43 Mbp
50 32 7.77 Mbp 11 36.31 Mbp
60 45 5.58 Mbp 13 35.05 Mbp
70 61 4.49 Mbp 16 33.11 Mbp
80 85 2.74 Mbp 18 30.53 Mbp
90 130 1.26 Mbp 21 27.21 Mbp
100 674 141 bp 203 6.74 Kbp
1.000x 674 0.83 Gbp 203 0.83 Gbp
NG based on genome size 0.83 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 26 July 2024
fSebFas1.alt.cur.20240726.fasta.gz (219.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 194 329.47 Kbp 194 329.47 Kbp
20 502 233.00 Kbp 502 233.00 Kbp
30 904 187.20 Kbp 904 187.20 Kbp
40 1409 148.13 Kbp 1409 148.13 Kbp
50 2035 120.39 Kbp 2035 120.39 Kbp
60 2816 94.50 Kbp 2816 94.50 Kbp
70 3820 72.40 Kbp 3820 72.40 Kbp
80 5202 50.19 Kbp 5202 50.19 Kbp
90 7346 30.08 Kbp 7346 30.08 Kbp
100 11377 3.22 Kbp 11377 3.22 Kbp
1.000x 11377 0.83 Gbp 11377 0.83 Gbp
NG based on genome size 0.83 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/fSebFas1.yml (view)
species: Sebastes fasciatus
specimen: fSebFas1
projects: 
  - vgp
data_location: S3
release_to: S3
primary: s3://genomeark/species/Sebastes_fasciatus/fSebFas1/assembly_vgp_standard_2.0/fSebFas1.standard.pri.20231115.fasta.gz
haplotigs: s3://genomeark/species/Sebastes_fasciatus/fSebFas1/assembly_vgp_standard_2.0/fSebFas1.standard.alt.20231115.fasta.gz
pretext: s3://genomeark/species/Sebastes_fasciatus/fSebFas1/assembly_vgp_standard_2.0/evaluation/pri/pretext/fSebFas1_pri__s2.heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Sebastes_fasciatus/fSebFas1/assembly_vgp_standard_2.0/evaluation/merqury/fSebFas1_png/
pacbio_read_dir: s3://genomeark/species/Sebastes_fasciatus/fSebFas1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Sebastes_fasciatus/fSebFas4/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a primary/alternate assembly of fSebFas1. This individual did not have bionano data. The HiC data came from a different individual, fSebFas4. HiC scaffolding was performed with yahs. The HiC prep was Arima. After purging, merqury plots show some potential false duplications in the alternate assembly. These were not removed even after a second round of purging on the alternate assembly, so the original alternate assembly (i.e., not twice-purged) is uploaded. 
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.