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_curated from 18 November 2025
fPemSco2.hap1.cur.20251118.fasta.gz (182.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 15.03 Mbp 2 35.40 Mbp
20 11 11.36 Mbp 5 32.80 Mbp
30 18 9.62 Mbp 7 32.30 Mbp
40 26 8.42 Mbp 9 31.01 Mbp
50 36 6.82 Mbp 12 29.11 Mbp
60 49 4.38 Mbp 14 28.00 Mbp
70 71 2.67 Mbp 17 26.62 Mbp
80 112 1.25 Mbp 20 25.10 Mbp
90 212 465.97 Kbp 23 17.68 Mbp
100 860 10.51 Kbp 538 10.51 Kbp
1.000x 860 0.75 Gbp 538 0.75 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 18 November 2025
fPemSco2.hap2.cur.20251118.fasta.gz (179.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 13.90 Mbp 2 32.92 Mbp
20 11 11.51 Mbp 5 30.96 Mbp
30 18 9.86 Mbp 7 29.56 Mbp
40 26 7.81 Mbp 10 28.83 Mbp
50 37 6.03 Mbp 12 27.76 Mbp
60 51 4.09 Mbp 15 26.63 Mbp
70 75 2.50 Mbp 18 24.54 Mbp
80 119 1.20 Mbp 21 21.22 Mbp
90 214 497.09 Kbp 33 1.35 Mbp
100 760 13.07 Kbp 485 13.07 Kbp
1.000x 760 0.73 Gbp 485 0.73 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 14 October 2024
fPemSch2.MT.20241014.fasta.gz (5.3 KiB)

Quality: not computed
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.