Mustela nivalis

least weasel

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  short_name: mMusNiv
  name: Mustela nivalis
  taxon_id: 36239
  common_name: least weasel
  order:
    name: Carnivora
  family:
    name: Mustelidae
  individuals:
    - short_name: mMusNiv2
      biosample_id: SAMEA113398841
      sex: female
  genome_size: 3012240000
  genome_size_method: GoaT
  project: [ vgp ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mMusNiv1 2421.40 Gbp 803.85x 4.1 TiB
PacBio HiFi (.fq) mMusNiv1 83.82 Gbp 27.83x 62.2 GiB
PacBio HiFi (.bam) mMusNiv2 103.63 Gbp 34.40x 28.7 GiB
Arima mMusNiv1 269.37 Gbp 89.43x 138.4 GiB
mMusNiv2 541.15 Gbp 179.65x 150.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.01 Gbp.
Last upload on 20 July 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMusNiv1 PacBio HiFi (subreads) 2421.40 Gbp 803.85x 4.1 TiB
PacBio HiFi (.fq) 83.82 Gbp 27.83x 62.2 GiB
Arima 269.37 Gbp 89.43x 138.4 GiB
mMusNiv2 PacBio HiFi (.bam) 103.63 Gbp 34.40x 28.7 GiB
Arima 541.15 Gbp 179.65x 150.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.01 Gbp.
Last upload on 20 July 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 15 December 2023
mMusNiv1.HiC.hap1.20231215.fasta.gz (820.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 67.00 Mbp 2 223.56 Mbp
20 8 55.47 Mbp 3 176.68 Mbp
30 14 43.94 Mbp 5 166.28 Mbp
40 23 29.34 Mbp 7 152.14 Mbp
50 36 18.36 Mbp 9 114.87 Mbp
60 56 11.50 Mbp 12 98.22 Mbp
70 94 5.37 Mbp 15 70.56 Mbp
80 198 1.51 Mbp 35 3.66 Mbp
90 834 220.22 Kbp 473 249.34 Kbp
100 4759 10.26 Kbp 4313 10.26 Kbp
1.000x 4759 3.00 Gbp 4313 3.01 Gbp
NG based on genome size 3.01 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 15 December 2023
mMusNiv1.HiC.hap2.20231215.fasta.gz (853.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 91.13 Mbp 2 176.64 Mbp
20 7 64.43 Mbp 4 159.27 Mbp
30 13 44.96 Mbp 6 154.67 Mbp
40 22 30.57 Mbp 8 137.01 Mbp
50 34 21.73 Mbp 11 114.46 Mbp
60 51 12.32 Mbp 14 92.52 Mbp
70 85 5.74 Mbp 17 70.43 Mbp
80 187 1.54 Mbp 30 6.35 Mbp
90 810 218.43 Kbp 473 243.53 Kbp
100 4796 14.40 Kbp 4400 14.40 Kbp
1.000x 4796 3.11 Gbp 4400 3.13 Gbp
NG based on genome size 3.01 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 December 2023
mMusNiv1.MT.20231215.fasta.gz (5.3 KiB)

Quality: not computed
Individual 2 Haplotype 1 Assembly
Version assembly_cambridge from 2 October 2024
mMusNiv2.hap1.asm.20241002.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 74 3.19 Mbp 2 163.28 Mbp
20 183 2.42 Mbp 4 147.43 Mbp
30 322 1.97 Mbp 6 143.31 Mbp
40 493 1.59 Mbp 8 117.19 Mbp
50 699 1.34 Mbp 11 108.72 Mbp
60 947 1.10 Mbp 14 91.73 Mbp
70 1252 0.89 Mbp 18 62.33 Mbp
80 1636 0.69 Mbp 28 5.33 Mbp
90 2143 0.51 Mbp 165 1.48 Mbp
100 2873 322.00 Kbp 478 0.62 Mbp
1.137x 6086 3.42 Gbp 3267 3.43 Gbp
NG based on genome size 3.01 Gbp.
Individual 2 Haplotype 2 Assembly
Version assembly_cambridge from 2 October 2024
mMusNiv2.hap2.asm.20241002.fasta.gz (785.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 81 2.94 Mbp 2 163.03 Mbp
20 201 2.19 Mbp 4 148.86 Mbp
30 359 1.69 Mbp 6 143.42 Mbp
40 558 1.37 Mbp 8 113.97 Mbp
50 802 1.10 Mbp 11 106.44 Mbp
60 1113 0.87 Mbp 15 85.03 Mbp
70 1515 0.65 Mbp 19 58.52 Mbp
80 2082 429.44 Kbp 80 1.69 Mbp
90 3146 165.05 Kbp 552 243.77 Kbp
100 0 0
0.946x 5019 2.85 Gbp 2342 2.85 Gbp
NG based on genome size 3.01 Gbp.
Individual 2 Mitochondrial Assembly
Version assembly_MT_cambridge from 2 October 2024
mMusNiv2.MT.20241002.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mMusNiv1.yml (view)
species: Mustela nivalis vulgaris
specimen: mMusNiv1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
hap1: s3://genomeark/species/Mustela_nivalis/mMusNiv1/assembly_vgp_HiC_2.0/mMusNiv1.HiC.hap1.20231215.fasta.gz
hap2: s3://genomeark/species/Mustela_nivalis/mMusNiv1/assembly_vgp_HiC_2.0/mMusNiv1.HiC.hap2.20231215.fasta.gz
pretext_hap1: s3://genomeark/species/Mustela_nivalis/mMusNiv1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mMusNiv1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Mustela_nivalis/mMusNiv1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mMusNiv1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Mustela_nivalis/mMusNiv1/assembly_vgp_HiC_2.0/evaluation/merqury/mMusNiv1_png/
pacbio_read_dir: s3://genomeark/species/Mustela_nivalis/mMusNiv1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Mustela_nivalis/mMusNiv1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Mustela_nivalis/mMusNiv1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mMusNiv1, 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. This sample did have bionano data. Final genome size looks large compared to existing assembly, likely because of fragmented repetitive regions captured by HiFi (but not scaffolded), which were missed with previous sequencing technologies. 
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.