Mustela nivalis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mMusNiv1 83.82 Gbp N/A 62.2 GiB
Arima mMusNiv1 269.37 Gbp N/A 138.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 September 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMusNiv1 PacBio HiFi (.fq) 83.82 Gbp N/A 62.2 GiB
Arima 269.37 Gbp N/A 138.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 September 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 15 December 2023
mMusNiv1.HiC.hap1.decontam.20231215.fasta.gz (741.4 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
80 197 1.54 Mbp 35 3.66 Mbp
90 831 220.93 Kbp 470 250.09 Kbp
100 4717 10.26 Kbp 4271 10.26 Kbp
1.000x 4717 3.00 Gbp 4271 3.01 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 15 December 2023
mMusNiv1.HiC.hap2.decontam.20231215.fasta.gz (771.3 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 13 95.04 Mbp
70 85 5.74 Mbp 17 70.43 Mbp
80 186 1.54 Mbp 30 6.35 Mbp
90 806 220.40 Kbp 470 244.90 Kbp
100 4752 14.40 Kbp 4356 14.40 Kbp
1.000x 4752 3.11 Gbp 4356 3.13 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 December 2023
mMusNiv1.MT.20231215.fasta.gz (5.3 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.