Sebastes mentella

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fSebMen1 42.94 Gbp N/A 18.6 GiB
PacBio HiFi (.bam) fSebMen1 396.41 Gbp N/A 171.8 GiB
Arima fSebMen1 272.02 Gbp N/A 141.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fSebMen1 PacBio HiFi (.fq) 42.94 Gbp N/A 18.6 GiB
PacBio HiFi (.bam) 396.41 Gbp N/A 171.8 GiB
Arima 272.02 Gbp N/A 141.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 11 December 2023
fSebMen1.HiC.hap1.20231211.fasta.gz (233.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 17.21 Mbp 2 41.85 Mbp
20 9 14.09 Mbp 4 40.27 Mbp
30 16 11.54 Mbp 7 36.17 Mbp
40 24 8.92 Mbp 9 35.58 Mbp
50 35 6.69 Mbp 11 34.73 Mbp
60 49 5.10 Mbp 14 32.23 Mbp
70 68 3.66 Mbp 16 32.17 Mbp
80 97 2.24 Mbp 19 28.16 Mbp
90 155 0.88 Mbp 22 26.15 Mbp
100 917 7.54 Kbp 520 7.54 Kbp
1.000x 917 0.82 Gbp 520 0.82 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 11 December 2023
fSebMen1.HiC.hap2.20231211.fasta.gz (234.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 18.93 Mbp 2 42.31 Mbp
20 9 15.76 Mbp 5 38.73 Mbp
30 16 11.27 Mbp 7 36.26 Mbp
40 24 9.00 Mbp 9 35.72 Mbp
50 35 6.97 Mbp 11 35.25 Mbp
60 48 5.92 Mbp 14 33.67 Mbp
70 65 3.81 Mbp 16 32.63 Mbp
80 91 2.44 Mbp 19 28.33 Mbp
90 146 0.86 Mbp 22 27.06 Mbp
100 777 7.08 Kbp 370 7.08 Kbp
1.000x 777 0.83 Gbp 370 0.83 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/fSebMen1.yml (view)
species: Sebastes mantella
specimen: fSebMen1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Sebastes_mantella/fSebMen1/assembly_vgp_HiC_2.0/fSebMen1.HiC.hap1.20231211.fasta.gz
hap2: s3://genomeark/species/Sebastes_mantella/fSebMen1/assembly_vgp_HiC_2.0/fSebMen1.HiC.hap2.20231211.fasta.gz
pretext_hap1: s3://genomeark/species/Sebastes_mantella/fSebMen1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fSebMen1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Sebastes_mantella/fSebMen1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fSebMen1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Sebastes_mantella/fSebMen1/assembly_vgp_HiC_2.0/evaluation/merqury/fSebMen1_png/
pacbio_read_dir: s3://genomeark/species/Sebastes_mantella/fSebMen1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Sebastes_mantella/fSebMen1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fSebMen1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS. The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. This is a VGP Phase 1 species we are submitting for dual curation.
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.