Canis lupus

gray wolf

Included in the VGP and T2T.

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


metadata.yaml (view) (edit on github)
species:
  short_name: mCanLup
  name: Canis lupus
  taxon_id: 9612
  common_name: gray wolf
  order:
    name: Carnivora
  family:
    name: Canidae
  individuals:
  -
     short_name: mCanLor1
     subspecies:
       name: Canis lupus orion
       common_name: Greenland wolf
       taxon_id: 2605939
     project: [ vgp ]
  -
     short_name: mCanLup5
     name:  Alfie
     biosample_id: null
     strain: null
     breed: Labrador retriever
     subspecies:
       name: Canis lupus familiaris
       common_name: dog
       taxon_id: 9615
     alt_ids:
     -  339608
     sex: male
     description: null
     provider: Jeff Schoenebeck (The Roslin Institute, University of Edinburgh)
     mother: null
     father: null
     project: [ t2t ]
     samples:
     -
        sample_id: mCanLup5.stomachbody1
        tissue: stomach body
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 1
        preservation_method: RNAlater
        extraction_date: 2024-10-13
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.skin1
        tissue: skin
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 2
        preservation_method: RNAlater
        extraction_date: 2024-10-13
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.retina1
        tissue: retina
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 3
        preservation_method: RNAlater
        extraction_date: 2024-10-13
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.trachealcartilage1
        tissue: tracheal cartilage
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 4
        preservation_method: RNAlater
        extraction_date: 2024-10-13
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.liver1
        tissue: liver
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 5
        preservation_method: RNAlater
        extraction_date: 2024-10-13
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.ileum1
        tissue: ileum
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 6
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.adrenalmedulla1
        tissue: adrenal medulla
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 7
        preservation_method: snap frozen
        extraction_date: 2024-10-17
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.skeletalmuscle1
        tissue: skeletal muscle
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 8
        preservation_method: RNAlater
        extraction_date: 2024-10-17
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.scapularlymphgland1
        tissue: scapular lymph gland
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 9
        preservation_method: RNAlater
        extraction_date: 2024-10-17
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.kidneycortex1
        tissue: kidney cortex
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 10
        preservation_method: RNAlater
        extraction_date: 2024-10-17
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.heart1
        tissue: heart
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 11
        preservation_method: RNAlater
        extraction_date: 2024-10-17
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.bonemarrow1
        tissue: bone marrow
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 12
        preservation_method: RNAlater
        extraction_date: 2024-10-17
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.frontallobcortex1
        tissue: frontal lobe cortex
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 13
        preservation_method: RNAlater
        extraction_date: 2024-10-17
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.cerebellum1
        tissue: cerebellum
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 14
        preservation_method: RNAlater
        extraction_date: 2024-10-17
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.spleen1
        tissue: spleen
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 15
        preservation_method: RNAlater
        extraction_date: 2024-10-19
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.descendingcolon1
        tissue: descending colon
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 16
        preservation_method: RNAlater
        extraction_date: 2024-10-19
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.palatemuscle1
        tissue: palate (muscle)
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 17
        preservation_method: RNAlater
        extraction_date: 2024-10-19
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.palateepithelium1
        tissue: palate epithelium
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 18
        preservation_method: RNAlater
        extraction_date: 2024-10-19
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.stomachbody2
        tissue: stomach body
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 75
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.skin2
        tissue: skin
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 76
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.retina2
        tissue: retina
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 77
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.trachealcartilage2
        tissue: tracheal cartilage
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 78
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.liver2
        tissue: liver
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 79
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.ileum2
        tissue: ileum
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 80
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.adrenalmedulla2
        tissue: adrenal medulla
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 81
        preservation_method: snap frozen
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.skeletalmuscle2
        tissue: skeletal muscle
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 82
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.scapularlymphgland2
        tissue: scapular lymph gland
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 83
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.kidneycortex2
        tissue: kidney cortex
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 84
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.heart2
        tissue: heart
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 85
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.bonemarrow2
        tissue: bone marrow
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 86
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.frontallobcortex2
        tissue: frontal lobe cortex
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 87
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.cerebellum2
        tissue: cerebellum
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 88
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.spleen2
        tissue: spleen
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 89
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.descendingcolon2
        tissue: descending colon
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 90
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.palatemuscle2
        tissue: palate (muscle)
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 91
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
     -
        sample_id: mCanLup5.palateepithelium2
        tissue: palate epithelium
        dev_stage: adult
        sample_biosample_id: null
        tube_number: 92
        preservation_method: RNAlater
        extraction_date: 2024-10-24
        provider: Jeff Schoenebeck, The Roslin Institute, University of Edinburgh
  genome_size: 3070000000
  genome_size_method: Genomes on a Tree (GoaT) estimate
  project: [ vgp, t2t ]
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mCanLup5 1293.24 Gbp 421.25x 2.1 TiB
PacBio HiFi (.fq) mCanLup2 87.08 Gbp 28.36x 43.2 GiB
mCanLup5 134.48 Gbp 43.80x 113.5 GiB
PacBio HiFi (.bam) mCanLup2 733.40 Gbp 238.89x 355.7 GiB
mCanLup5 137.54 Gbp 44.80x 285.2 GiB
Oxford Nanopore Simplex mCanLup5 432.54 Gbp 140.89x 338.9 GiB
10x mCanLup5 125.78 Gbp 40.97x 76.5 GiB
Arima mCanLup2 343.87 Gbp 112.01x 183.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.07 Gbp.
Last upload on 25 March 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mCanLup2 PacBio HiFi (.fq) 87.08 Gbp 28.36x 43.2 GiB
PacBio HiFi (.bam) 733.40 Gbp 238.89x 355.7 GiB
Arima 343.87 Gbp 112.01x 183.1 GiB
mCanLup5 PacBio HiFi (subreads) 1293.24 Gbp 421.25x 2.1 TiB
PacBio HiFi (.fq) 134.48 Gbp 43.80x 113.5 GiB
PacBio HiFi (.bam) 137.54 Gbp 44.80x 285.2 GiB
Oxford Nanopore Simplex 432.54 Gbp 140.89x 338.9 GiB
10x 125.78 Gbp 40.97x 76.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.07 Gbp.
Last upload on 25 March 2025.
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 3.07 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 3.07 Gbp.
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 10 February 2025
mCanLup2.hap1.cur.20250210.fasta.gz (711.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 59.23 Mbp 3 93.41 Mbp
20 9 45.71 Mbp 5 89.11 Mbp
30 14 41.32 Mbp 8 78.53 Mbp
40 21 35.57 Mbp 11 76.24 Mbp
50 28 31.96 Mbp 15 65.57 Mbp
60 37 23.18 Mbp 19 62.84 Mbp
70 49 18.45 Mbp 23 55.40 Mbp
80 65 12.77 Mbp 28 47.33 Mbp
90 92 6.29 Mbp 34 42.06 Mbp
100 416 4.30 Kbp 249 4.30 Kbp
1.000x 416 2.50 Gbp 249 2.50 Gbp
NG based on genome size 3.07 Gbp.
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 10 February 2025
mCanLup2.hap2.cur.20250210.fasta.gz (617.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 66.56 Mbp 3 90.07 Mbp
20 7 58.06 Mbp 5 87.13 Mbp
30 11 53.38 Mbp 8 76.98 Mbp
40 16 45.46 Mbp 11 71.85 Mbp
50 21 40.95 Mbp 15 64.06 Mbp
60 27 33.31 Mbp 19 59.74 Mbp
70 35 26.64 Mbp 23 53.38 Mbp
80 46 17.50 Mbp 27 46.50 Mbp
90 64 8.67 Mbp 33 40.95 Mbp
100 279 11.60 Kbp 155 11.60 Kbp
1.000x 279 2.34 Gbp 155 2.34 Gbp
NG based on genome size 3.07 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.