Manis pentadactyla

Chinese pangolin

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


Resource Primary Assembly Alternate Assembly
GenBank mManPen7: GCA_030020395.1 mManPen7: GCA_030020945.1
ENA mManPen7: GCA_030020395.1 mManPen7: GCA_030020945.1
UCSC Genome Browser mManPen7: GCA_030020395.1 mManPen7: GCA_030020945.1

metadata.yaml (view) (edit on github)
species:
  short_name: mManPen
  name: Manis pentadactyla
  taxon_id: 143292
  common_name: Chinese pangolin
  order:
    name: Pholidota
  family:
    name: Manidae
  individuals:
    - short_name: mManPen7
      provider: Shujin Luo, Bill Murphy
      sex: male
  genome_size: 2800000000
  genome_size_method: GoaT ancestral inferred
  project: [ vgp ]
CC BY-SA 4.0 A.J.T. Johnsingh, WWF-India and NCF (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mManPen7 354.82 Gbp 126.72x 801.5 GiB
PacBio HiFi (.fq) mManPen7 84.30 Gbp 30.11x 68.5 GiB
PacBio HiFi (.bam) mManPen7 85.21 Gbp 30.43x 295.2 GiB
Bionano mManPen7 N/A 275.61x 1.4 GiB
Dovetail Genomics mManPen7 257.11 Gbp 91.83x 133.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.80 Gbp.
Last upload on 23 November 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mManPen7 PacBio HiFi (subreads) 354.82 Gbp 126.72x 801.5 GiB
PacBio HiFi (.fq) 84.30 Gbp 30.11x 68.5 GiB
PacBio HiFi (.bam) 85.21 Gbp 30.43x 295.2 GiB
Bionano N/A 275.61x 1.4 GiB
Dovetail Genomics 257.11 Gbp 91.83x 133.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.80 Gbp.
Last upload on 23 November 2022.
Assemblies
Individual 7 Haplotype 1 Assembly
Version assembly_curated from 6 April 2023
mManPen7.hap1.cur.20230406.fasta.gz (783.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 104.11 Mbp 2 236.45 Mbp
20 6 68.14 Mbp 3 221.94 Mbp
30 11 50.91 Mbp 4 190.95 Mbp
40 17 36.51 Mbp 6 167.00 Mbp
50 26 25.71 Mbp 8 149.55 Mbp
60 38 22.07 Mbp 9 141.14 Mbp
70 52 15.80 Mbp 12 124.88 Mbp
80 73 10.06 Mbp 14 108.20 Mbp
90 122 3.11 Mbp 17 80.29 Mbp
100 512 164.75 Kbp 124 251.79 Kbp
1.012x 1044 2.83 Gbp 661 2.84 Gbp
NG based on genome size 2.80 Gbp.
Individual 7 Haplotype 2 Assembly
Version assembly_curated from 6 April 2023
mManPen7.hap2.decon.20230406.fasta.gz (783.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 152.66 Mbp 2 223.42 Mbp
20 5 68.30 Mbp 3 219.24 Mbp
30 9 57.26 Mbp 4 186.78 Mbp
40 15 40.23 Mbp 6 153.65 Mbp
50 23 31.35 Mbp 8 139.39 Mbp
60 32 25.31 Mbp 10 123.59 Mbp
70 45 19.37 Mbp 13 102.57 Mbp
80 63 11.94 Mbp 16 76.89 Mbp
90 105 3.22 Mbp 20 31.49 Mbp
100 383 309.02 Kbp 189 477.06 Kbp
1.019x 890 2.85 Gbp 700 2.87 Gbp
NG based on genome size 2.80 Gbp.
Individual 7 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 February 2023
mManPen7.MT.20230210.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mManPen7.yaml (view)
species: Manis pentadactyla
specimen: mManPen7
projects: 
  - vgp
hap1: s3://genomeark/species/Manis_pentadactyla/mManPen7/assembly_vgp_HiC_2.0/mManPen7.HiC.hap1.20221222.fasta.gz
hap2: s3://genomeark/species/Manis_pentadactyla/mManPen7/assembly_vgp_HiC_2.0/mManPen7.HiC.hap2.20221222.fasta.gz
pretext_hap1: s3://genomeark/species/Manis_pentadactyla/mManPen7/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mManPen7_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Manis_pentadactyla/mManPen7/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mManPen7_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Manis_pentadactyla/mManPen7/assembly_vgp_HiC_2.0/evaluation/merqury/mManPen7_png/
pacbio_read_dir: s3://genomeark/species/Manis_pentadactyla/mManPen7/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Manis_pentadactyla/mManPen7/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Manis_pentadactyla/mManPen7/genomic_data/dovetail/
hic_kit: OmniC
pipeline:
  - hifiasm (0.16.1+galaxy3)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of mManPen7, resulting in two complete haplotypes. HiC scaffolding was performed with YAHS. The HiC prep was Dovetail OmniC. The kmer spectra indicates a heterogametic specimen. Becuase the sex chromosomes are split between the two haplotypes, we are including the file paths for both haplotypes in this single ticket.
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.