Pempheris schomburgkii

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fPemSco2 49.73 Gbp N/A 22.8 GiB
PacBio HiFi (.bam) fPemSco2 50.46 Gbp N/A 166.5 GiB
Arima fPemSco2 55.73 Gbp N/A 29.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 October 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fPemSco2 PacBio HiFi (.fq) 49.73 Gbp N/A 22.8 GiB
PacBio HiFi (.bam) 50.46 Gbp N/A 166.5 GiB
Arima 55.73 Gbp N/A 29.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 October 2024.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 14 October 2024
fPemSco2.HiC.hap1.20241014.fasta.gz (175.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 13.90 Mbp 2 33.10 Mbp
20 10 11.64 Mbp 4 28.71 Mbp
30 16 9.93 Mbp 7 27.76 Mbp
40 24 8.47 Mbp 9 27.30 Mbp
50 33 6.53 Mbp 12 25.62 Mbp
60 44 5.69 Mbp 15 24.80 Mbp
70 63 2.75 Mbp 18 22.27 Mbp
80 95 1.44 Mbp 21 20.20 Mbp
90 185 462.55 Kbp 39 0.91 Mbp
100 804 9.88 Kbp 585 9.88 Kbp
1.000x 804 0.69 Gbp 585 0.69 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 14 October 2024
fPemSco2.HiC.hap2.20241014.fasta.gz (187.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 15.03 Mbp 3 30.64 Mbp
20 11 11.36 Mbp 6 28.90 Mbp
30 19 9.62 Mbp 8 28.13 Mbp
40 28 8.16 Mbp 11 27.28 Mbp
50 39 6.12 Mbp 14 26.02 Mbp
60 56 3.78 Mbp 17 24.62 Mbp
70 83 2.19 Mbp 21 20.04 Mbp
80 134 1.16 Mbp 26 3.43 Mbp
90 238 478.21 Kbp 77 0.81 Mbp
100 819 8.62 Kbp 567 8.62 Kbp
1.000x 819 0.79 Gbp 567 0.79 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/fPemSco2.yaml (view)
species: Pempheris schomburgkii
specimen: fPemSco2
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Pempheris_schomburgkii/fPemSco2/assembly_vgp_HiC_2.0/fPemSco2.HiC.hap1.20241014.fasta.gz 
hap2: s3://genomeark/species/Pempheris_schomburgkii/fPemSco2/assembly_vgp_HiC_2.0/fPemSco2.HiC.hap2.20241014.fasta.gz 
pretext_hap1: s3://genomeark/species/Pempheris_schomburgkii/fPemSco2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fPemSco2_hap1__s2_heatmap.pretext  
pretext_hap2: s3://genomeark/species/Pempheris_schomburgkii/fPemSco2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fPemSco2_hap2__s2_heatmap.pretext 
kmer_spectra_img: s3://genomeark/species/Pempheris_schomburgkii/fPemSco2/assembly_vgp_HiC_2.0/evaluation/merqury/fPemSco2_png/
pacbio_read_dir: s3://genomeark/species/Pempheris_schomburgkii/fPemSco2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pempheris_schomburgkii/fPemSco2/genomic_data/arima/
mito: s3://genomeark/species/Pempheris_schomburgkii/fPemSco2/assembly_MT_rockefeller/fPemSch2.MT.20241014.fasta.gz.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fPemSco2, 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.