Pangshura tecta

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rPanTec1 102.40 Gbp N/A 51.4 GiB
PacBio HiFi (.bam) rPanTec1 103.89 Gbp N/A 419.2 GiB
Arima rPanTec1 331.42 Gbp N/A 176.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 April 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rPanTec1 PacBio HiFi (.fq) 102.40 Gbp N/A 51.4 GiB
PacBio HiFi (.bam) 103.89 Gbp N/A 419.2 GiB
Arima 331.42 Gbp N/A 176.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 April 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 28 May 2024
rPanTec1.hap1.cur.20240528.fasta.gz (631.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 117.44 Mbp 1 353.78 Mbp
20 4 98.74 Mbp 2 284.19 Mbp
30 7 70.21 Mbp 3 201.05 Mbp
40 10 64.56 Mbp 4 145.02 Mbp
50 14 54.15 Mbp 5 136.65 Mbp
60 18 42.72 Mbp 7 123.25 Mbp
70 24 31.23 Mbp 9 101.70 Mbp
80 34 11.73 Mbp 11 75.85 Mbp
90 59 4.77 Mbp 17 26.36 Mbp
100 834 11.64 Kbp 629 11.64 Kbp
1.000x 834 2.17 Gbp 629 2.17 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 28 May 2024
rPanTec1.hap2.cur.20240528.fasta.gz (633.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 127.05 Mbp 1 354.21 Mbp
20 4 112.88 Mbp 2 284.08 Mbp
30 6 77.37 Mbp 3 202.57 Mbp
40 9 69.61 Mbp 4 145.06 Mbp
50 12 58.73 Mbp 5 135.94 Mbp
60 17 39.33 Mbp 7 123.50 Mbp
70 24 26.71 Mbp 9 101.81 Mbp
80 36 11.06 Mbp 11 76.05 Mbp
90 64 5.11 Mbp 17 25.43 Mbp
100 708 13.74 Kbp 448 13.74 Kbp
1.000x 708 2.17 Gbp 448 2.17 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 30 April 2024
rPanTec1.MT.20240430.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rPanTec1.yml (view)
species: Pangshura tecta
specimen: rPanTec1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Pangshura_tecta/rPanTec1/assembly_vgp_HiC_2.0/rPanTec1.HiC.hap1.20240430.fasta.gz
hap2: s3://genomeark/species/Pangshura_tecta/rPanTec1/assembly_vgp_HiC_2.0/rPanTec1.HiC.hap2.20240430.fasta.gz
pretext_hap1: s3://genomeark/species/Pangshura_tecta/rPanTec1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rPanTec1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Pangshura_tecta/rPanTec1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rPanTec1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Pangshura_tecta/rPanTec1/assembly_vgp_HiC_2.0/evaluation/merqury/rPanTec1_png/
pacbio_read_dir: s3://genomeark/species/Pangshura_tecta/rPanTec1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pangshura_tecta/rPanTec1/genomic_data/arima/
mito: s3://genomeark/species/Pangshura_tecta/rPanTec1/assembly_MT_rockefeller/rPanTec1.MT.20240430.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of rPanTec1, 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.