Nycticebus coucang

slow loris

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank mNycCou1: GCA_027406575.1 mNycCou1: GCA_027406535.1
ENA mNycCou1: GCA_027406575.1 mNycCou1: GCA_027406535.1
UCSC Genome Browser mNycCou1: GCA_027406575.1 mNycCou1: GCA_027406535.1

metadata.yaml (view) (edit on github)
species:
  name: Nycticebus coucang
  individuals:
  - short_name: mNycCou1
  short_name: mNycCou
  taxon_id: 9470
  common_name: slow loris
  genome_size: 3501000000
  genome_size_method: GoAT
  order:
    name: Primates
  family:
    name: Lorisidae
  project: [ vgp ]
CC BY-SA 3.0 David Haring/Duke Lemur Center (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mNycCou1 388.50 Gbp 110.97x 0.9 TiB
PacBio HiFi (.fq) mNycCou1 110.73 Gbp 31.63x 84.1 GiB
PacBio HiFi (.bam) mNycCou1 110.77 Gbp 31.64x 377.6 GiB
Bionano mNycCou1 N/A 387.42x 2.9 GiB
Arima mNycCou1 289.27 Gbp 82.62x 146.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.50 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mNycCou1 PacBio HiFi (subreads) 388.50 Gbp 110.97x 0.9 TiB
PacBio HiFi (.fq) 110.73 Gbp 31.63x 84.1 GiB
PacBio HiFi (.bam) 110.77 Gbp 31.64x 377.6 GiB
Bionano N/A 387.42x 2.9 GiB
Arima 289.27 Gbp 82.62x 146.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.50 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 1 April 2022
mNycCou1.pri.cur.20220401.fasta.gz (845.5 MiB)

Quality: 0.1 errors/Mb (QV=68.35)

Contigs Scaffolds
NG LG Len LG Len
10 3 82.19 Mbp 1 187.33 Mbp
20 8 74.33 Mbp 3 161.20 Mbp
30 13 56.61 Mbp 6 138.33 Mbp
40 21 41.58 Mbp 8 136.59 Mbp
50 30 31.79 Mbp 11 128.24 Mbp
60 43 23.37 Mbp 14 99.99 Mbp
70 62 13.64 Mbp 18 80.58 Mbp
80 116 2.76 Mbp 23 38.95 Mbp
90 0 0
100 0 0
0.832x 302 2.91 Gbp 84 2.92 Gbp
NG based on genome size 3.50 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 1 April 2022
mNycCou1.alt.cur.20220401.fasta.gz (782.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 39 6.86 Mbp 39 6.86 Mbp
20 109 3.88 Mbp 109 3.88 Mbp
30 229 2.32 Mbp 229 2.32 Mbp
40 426 1.37 Mbp 426 1.37 Mbp
50 762 0.81 Mbp 762 0.81 Mbp
60 1347 456.04 Kbp 1347 456.04 Kbp
70 2535 171.41 Kbp 2535 171.41 Kbp
80 0 0
90 0 0
100 0 0
0.769x 6485 2.69 Gbp 6485 2.69 Gbp
NG based on genome size 3.50 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 June 2022
mNycCou1.MT.20220615.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/mNycCou1.yaml (view)
species: Nycticebus coucang
specimen: mNycCou1
projects:
  - vgp
primary: s3://genomeark/species/Nycticebus_coucang/mNycCou1/assembly_vgp_standard_2.0/mNycCou1.pri.asm.20220201.fasta.gz
haplotigs: s3://genomeark/species/Nycticebus_coucang/mNycCou1/assembly_vgp_standard_2.0/mNycCou1.alt.asm.20220201.fasta.gz
hic_bam: s3://genomeark/species/Nycticebus_coucang/mNycCou1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mNycCou1_s2.bam
pretext: s3://genomeark/species/Nycticebus_coucang/mNycCou1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mNycCou1_s2.pretext
kmer_spectra_img: s3://genomeark/species/Nycticebus_coucang/mNycCou1/assembly_vgp_standard_2.0/evaluation/merqury/p/mNycCou1_p1p2_images/
pipeline:
  - hifiasm (0.16.1-r375)
  - purge_dups (1.2.5)
  - solve (3.6.1)
  - salsa (2.2)
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.