Myoxocephalus scorpius

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fMyoSco1 43.68 Gbp N/A 34.7 GiB
Arima fMyoSco1 160.18 Gbp N/A 86.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 29 June 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fMyoSco1 PacBio HiFi (.fq) 43.68 Gbp N/A 34.7 GiB
Arima 160.18 Gbp N/A 86.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 29 June 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 18 July 2023
fMyoSco1.HiC.hap1.20230718.fasta.gz (198.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 9.15 Mbp 2 56.58 Mbp
20 16 6.57 Mbp 3 53.07 Mbp
30 28 5.66 Mbp 4 52.05 Mbp
40 43 4.14 Mbp 6 38.12 Mbp
50 63 3.08 Mbp 8 36.38 Mbp
60 89 2.49 Mbp 10 35.28 Mbp
70 123 1.80 Mbp 12 32.09 Mbp
80 173 1.12 Mbp 14 30.75 Mbp
90 259 0.61 Mbp 17 26.51 Mbp
100 585 17.14 Kbp 98 17.14 Kbp
1.000x 585 0.72 Gbp 98 0.72 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 18 July 2023
fMyoSco1.HiC.hap2.20230718.fasta.gz (199.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 7.44 Mbp 2 55.75 Mbp
20 20 5.62 Mbp 3 53.98 Mbp
30 34 4.57 Mbp 4 53.07 Mbp
40 51 4.05 Mbp 6 37.57 Mbp
50 71 3.03 Mbp 8 36.61 Mbp
60 99 2.26 Mbp 10 33.25 Mbp
70 136 1.71 Mbp 12 32.48 Mbp
80 188 1.13 Mbp 14 30.64 Mbp
90 275 0.60 Mbp 17 22.51 Mbp
100 591 10.35 Kbp 107 10.35 Kbp
1.000x 591 0.72 Gbp 107 0.72 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 18 July 2023
fMyoSco1.MT.20230718.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fMyoSco1.yml (view)
species: Myoxocephalus scorpius
specimen: fMyoSco1
projects: 
  - vgp
hap1: s3://genomeark/species/Myoxocephalus_scorpius/fMyoSco1/assembly_vgp_HiC_2.0/fMyoSco1.HiC.hap1.20230718.fasta.gz
hap2: s3://genomeark/species/Myoxocephalus_scorpius/fMyoSco1/assembly_vgp_HiC_2.0/fMyoSco1.HiC.hap2.20230718.fasta.gz
pretext_hap1: s3://genomeark/species/Myoxocephalus_scorpius/fMyoSco1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fMyoSco1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Myoxocephalus_scorpius/fMyoSco1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fMyoSco1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Myoxocephalus_scorpius/fMyoSco1/assembly_vgp_HiC_2.0/evaluation/merqury/fMyoSco1_png/
mito: s3://genomeark/species/Myoxocephalus_scorpius/fMyoSco1/assembly_MT_rockefeller/fMyoSco1.MT.20230718.fasta.gz
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (2.2)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of fMyoSco1, resulting in two complete haplotypes. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. The initial contig assemblies went through purging before scaffolding. 
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.