Neofelis nebulosa

Clouded leopard

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank mNeoNeb1: GCA_028018385.1 mNeoNeb1: GCA_028018655.1
ENA mNeoNeb1: GCA_028018385.1 mNeoNeb1: GCA_028018655.1
UCSC Genome Browser mNeoNeb1: GCA_028018385.1 mNeoNeb1: GCA_028018655.1

metadata.yaml (view) (edit on github)
species:
  name: Neofelis nebulosa
  individuals:
  - short_name: mNeoNeb1
  short_name: mNeoNeb
  taxon_id: '61452'
  common_name: Clouded leopard
  genome_size: 2709000000
  genome_size_method: GoAT
  order:
    name: Carnivora
  family:
    name: Felidae
  project: [ vgp ]
CC BY-SA 3.0 Trisha Shears (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mNeoNeb1 342.17 Gbp 126.31x 788.0 GiB
PacBio HiFi (.fq) mNeoNeb1 87.23 Gbp 32.20x 68.3 GiB
PacBio HiFi (.bam) mNeoNeb1 87.25 Gbp 32.21x 302.1 GiB
Bionano mNeoNeb1 N/A 238.14x 1.1 GiB
Arima mNeoNeb1 352.56 Gbp 130.14x 166.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.71 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mNeoNeb1 PacBio HiFi (subreads) 342.17 Gbp 126.31x 788.0 GiB
PacBio HiFi (.fq) 87.23 Gbp 32.20x 68.3 GiB
PacBio HiFi (.bam) 87.25 Gbp 32.21x 302.1 GiB
Bionano N/A 238.14x 1.1 GiB
Arima 352.56 Gbp 130.14x 166.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.71 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 20 May 2022
mNeoNeb1.pri.cur.20220520.fasta.gz (716.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 142.14 Mbp 1 222.43 Mbp
20 4 91.74 Mbp 2 207.47 Mbp
30 8 61.80 Mbp 3 170.16 Mbp
40 12 57.54 Mbp 5 156.03 Mbp
50 18 37.03 Mbp 7 143.00 Mbp
60 26 26.78 Mbp 9 128.49 Mbp
70 38 17.01 Mbp 11 95.68 Mbp
80 61 9.78 Mbp 14 83.65 Mbp
90 140 1.07 Mbp 18 46.37 Mbp
100 0 0
0.911x 214 2.47 Gbp 33 2.47 Gbp
NG based on genome size 2.71 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 20 May 2022
mNeoNeb1.alt.cur.20220520.fasta.gz (575.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 210 0.92 Mbp 210 0.92 Mbp
20 574 0.62 Mbp 574 0.62 Mbp
30 1082 460.02 Kbp 1082 460.02 Kbp
40 1765 342.35 Kbp 1765 342.35 Kbp
50 2707 240.72 Kbp 2707 240.72 Kbp
60 4145 144.32 Kbp 4145 144.32 Kbp
70 7484 41.70 Kbp 7484 41.70 Kbp
80 0 0
90 0 0
100 0 0
0.731x 10377 1.98 Gbp 10377 1.98 Gbp
NG based on genome size 2.71 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 June 2022
mNeoNeb1.MT.20220615.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/mNeoNeb1.yaml (view)
species: Neofelis nebulosa
specimen: mNeoNeb1
projects:
 - vgp
primary: s3://genomeark/species/Neofelis_nebulosa/mNeoNeb1/assembly_vgp_standard_2.0/mNeoNeb1.pri.asm.20220405.fasta.gz
haplotigs: s3://genomeark/species/Neofelis_nebulosa/mNeoNeb1/assembly_vgp_standard_2.0/mNeoNeb1.alt.asm.20220405.fasta.gz
hic_bam: s3://genomeark/species/Neofelis_nebulosa/mNeoNeb1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mNeoNeb1_s2.bam
pretext: s3://genomeark/species/Neofelis_nebulosa/mNeoNeb1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mNeoNeb1_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Neofelis_nebulosa/mNeoNeb1/assembly_vgp_standard_2.0/evaluation/merqury/p/mNeoNeb1_png/
pipeline:
  - hifiasm (0.16.1+galaxy2)
  - purge_dups (1.2.5+galaxy4)
  - solve (3.7.0+galaxy0)
  - salsa (2.3+galaxy2)
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.