Chaetodon trifascialis

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CC BY-SA 4.0 Julien Bidet for MDC Seamarc (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fChaTrf1 40.58 Gbp N/A 31.6 GiB
Arima fChaTrf1 69.47 Gbp N/A 32.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fChaTrf1 PacBio HiFi (.fq) 40.58 Gbp N/A 31.6 GiB
Arima 69.47 Gbp N/A 32.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 15 July 2023
fChaTrf1.hap1.decontam.20230715.fasta.gz (177.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 29.67 Mbp 2 35.13 Mbp
20 5 26.84 Mbp 4 31.51 Mbp
30 7 25.68 Mbp 6 31.22 Mbp
40 10 24.13 Mbp 8 30.57 Mbp
50 13 21.33 Mbp 10 29.77 Mbp
60 16 18.04 Mbp 12 28.03 Mbp
70 21 11.94 Mbp 15 26.06 Mbp
80 27 9.54 Mbp 17 24.69 Mbp
90 35 6.64 Mbp 20 22.24 Mbp
100 82 19.31 Kbp 35 19.31 Kbp
1.000x 82 0.66 Gbp 35 0.66 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 15 July 2023
fChaTrf1.hap2.decontam.20230715.fasta.gz (177.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 29.17 Mbp 2 33.05 Mbp
20 5 25.98 Mbp 5 31.57 Mbp
30 8 24.32 Mbp 7 30.64 Mbp
40 11 21.17 Mbp 9 29.75 Mbp
50 14 18.00 Mbp 11 28.16 Mbp
60 18 15.21 Mbp 14 27.19 Mbp
70 23 12.01 Mbp 16 26.16 Mbp
80 29 10.01 Mbp 19 24.54 Mbp
90 37 6.59 Mbp 21 22.41 Mbp
100 112 23.73 Kbp 70 23.73 Kbp
1.000x 112 0.66 Gbp 70 0.66 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 July 2023
fChaTrf1.MT.20230713.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fChaTrf1.yml (view)
species: Chaetodon trifascialis
specimen: fChaTrf1
projects: 
  - vgp
hap1: s3://genomeark/species/Chaetodon_trifascialis/fChaTrf1/assembly_vgp_HiC_2.0/fChaTrf1.HiC.hap1.20230713.fasta.gz
hap2: s3://genomeark/species/Chaetodon_trifascialis/fChaTrf1/assembly_vgp_HiC_2.0/fChaTrf1.HiC.hap2.20230713.fasta.gz
pretext_hap1: s3://genomeark/species/Chaetodon_trifascialis/fChaTrf1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fChaTrf1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Chaetodon_trifascialis/fChaTrf1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fChaTrf1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Chaetodon_trifascialis/fChaTrf1/assembly_vgp_HiC_2.0/evaluation/merqury/fChaTrf1_png/
mito: s3://genomeark/species/Chaetodon_trifascialis/fChaTrf1/assembly_MT_rockefeller/fChaTrf1.MT.20230713.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 fChaTrf1, 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.