Canis lupus

Greenland wolf

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank mCanLor1: GCA_905319855.2 mCanLor1: GCA_905319845.1
ENA mCanLor1: GCA_905319855.2 mCanLor1: GCA_905319845.1
UCSC Genome Browser mCanLor1: GCA_905319855.2 mCanLor1: GCA_905319845.1

metadata.yaml (view) (edit on github)
species:
  short_name: mCanLor
  name: Canis lupus
  taxon_id: 2605939
  common_name: Greenland wolf
  order:
    name: Carnivora
  family:
    name: Canidae
  individuals:
    - short_name: mCanLor1
  genome_size:
  genome_size_method:
  project: [ vgp ]
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.bam) mCanLor1 82.58 Gbp 33.74x 68.3 GiB
10x mCanLor1 283.59 Gbp 115.87x 167.9 GiB
Dovetail Genomics mCanLor1 116.58 Gbp 47.63x 72.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.45 Gbp.
Last upload on 12 October 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mCanLor1 PacBio HiFi (.bam) 82.58 Gbp 33.74x 68.3 GiB
10x 283.59 Gbp 115.87x 167.9 GiB
Dovetail Genomics 116.58 Gbp 47.63x 72.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.45 Gbp.
Last upload on 12 October 2023.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 15 March 2021
mCanLor1.pri.cur.20210315.fasta.gz (701.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 65.17 Mbp 1 122.96 Mbp
20 7 50.44 Mbp 4 88.63 Mbp
30 12 46.17 Mbp 7 78.39 Mbp
40 18 41.41 Mbp 10 73.73 Mbp
50 24 34.38 Mbp 14 65.78 Mbp
60 32 28.89 Mbp 18 62.79 Mbp
70 41 22.82 Mbp 22 53.62 Mbp
80 56 11.54 Mbp 27 46.11 Mbp
90 83 6.53 Mbp 32 41.77 Mbp
100 247 16.69 Kbp 81 16.69 Kbp
1.000x 248 2.45 Gbp 82 2.45 Gbp
NG based on genome size 2.45 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 15 March 2021
mCanLor1.alt.cur.20210315.fasta.gz (416.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 56 1.93 Mbp 56 1.93 Mbp
20 143 1.46 Mbp 143 1.46 Mbp
30 257 1.12 Mbp 257 1.12 Mbp
40 401 0.91 Mbp 401 0.91 Mbp
50 582 0.72 Mbp 582 0.72 Mbp
60 809 0.57 Mbp 809 0.57 Mbp
70 1106 423.16 Kbp 1106 423.16 Kbp
80 1522 279.47 Kbp 1522 279.47 Kbp
90 2239 135.75 Kbp 2239 135.75 Kbp
100 5536 4.83 Kbp 5535 4.83 Kbp
1.000x 5537 1.45 Gbp 5536 1.45 Gbp
NG based on genome size 2.45 Gbp.
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 13 November 2023
mCanLup2.hap1.decontam.20231113.fasta.gz (621.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 59.23 Mbp 3 89.56 Mbp
20 8 47.03 Mbp 5 86.81 Mbp
30 13 41.75 Mbp 8 77.17 Mbp
40 19 38.55 Mbp 12 65.59 Mbp
50 26 32.88 Mbp 15 65.18 Mbp
60 34 27.69 Mbp 19 59.14 Mbp
70 44 20.08 Mbp 23 53.22 Mbp
80 59 13.69 Mbp 28 44.64 Mbp
90 83 6.29 Mbp 33 42.06 Mbp
100 378 4.30 Kbp 256 4.30 Kbp
1.000x 378 2.36 Gbp 256 2.36 Gbp
NG based on genome size 2.45 Gbp.
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 13 November 2023
mCanLup2.hap2.decontam.20231113.fasta.gz (652.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 66.28 Mbp 2 123.63 Mbp
20 7 58.06 Mbp 5 88.67 Mbp
30 12 52.63 Mbp 8 78.25 Mbp
40 17 45.46 Mbp 11 72.98 Mbp
50 23 40.45 Mbp 15 65.76 Mbp
60 29 33.23 Mbp 19 61.97 Mbp
70 38 23.74 Mbp 23 53.60 Mbp
80 51 16.08 Mbp 28 45.46 Mbp
90 71 8.67 Mbp 34 40.95 Mbp
100 285 12.13 Kbp 187 12.13 Kbp
1.000x 285 2.47 Gbp 187 2.47 Gbp
NG based on genome size 2.45 Gbp.
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 November 2023
mCanLup2.MT.20231113.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mCanLup2_hap1.yml (view)
species: Canis lupus
specimen: mCanLup2
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_vgp_HiC_2.0/mCanLup2.HiC.hap1.20231107.fasta.gz
hap2: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_vgp_HiC_2.0/mCanLup2.HiC.hap2.20231107.fasta.gz
pretext_hap1: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mCanLup2_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mCanLup2_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_vgp_HiC_2.0/evaluation/merqury/mCanLup2_png/
pacbio_read_dir: s3://genomeark/species/Canis_lupus/mCanLup2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Canis_lupus/mCanLup2/genomic_data/arima/
mito: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_MT_rockefeller/mCanLup2.MT.20231113.fasta.gz
pipeline: 
  - hifiasm (0.16.1+galaxy4)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mCanLup2, 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. \n
assembly_vgp_HiC_2.0/mCanLup2_hap2.yml (view)
species: Canis lupus
specimen: mCanLup2
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_vgp_HiC_2.0/mCanLup2.HiC.hap1.20231107.fasta.gz
hap2: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_vgp_HiC_2.0/mCanLup2.HiC.hap2.20231107.fasta.gz
pretext_hap1: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mCanLup2_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mCanLup2_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_vgp_HiC_2.0/evaluation/merqury/mCanLup2_png/
pacbio_read_dir: s3://genomeark/species/Canis_lupus/mCanLup2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Canis_lupus/mCanLup2/genomic_data/arima/
mito: s3://genomeark/species/Canis_lupus/mCanLup2/assembly_MT_rockefeller/mCanLup2.MT.20231113.fasta.gz
pipeline: 
  - hifiasm (0.16.1+galaxy4)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mCanLup2, 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. \n
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.