Blarina brevicauda

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Resource Primary Assembly Alternate Assembly
GenBank mBlaBre1: GCA_051295465.1 mBlaBre1: GCA_051295425.1
ENA mBlaBre1: GCA_051295465.1 mBlaBre1: GCA_051295425.1
UCSC Genome Browser mBlaBre1: GCA_051295465.1 mBlaBre1: GCA_051295425.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mBlaBre2 128.39 Gbp N/A 61.1 GiB
PacBio HiFi (.bam) mBlaBre2 132.14 Gbp N/A 438.4 GiB
Arima mBlaBre2 123.21 Gbp N/A 65.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 July 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mBlaBre2 PacBio HiFi (.fq) 128.39 Gbp N/A 61.1 GiB
PacBio HiFi (.bam) 132.14 Gbp N/A 438.4 GiB
Arima 123.21 Gbp N/A 65.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 July 2025.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 7 October 2025
mBlaBre2.HiC.hap1.20251007.fasta.gz (608.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 9 22.48 Mbp 2 222.19 Mbp
20 23 13.37 Mbp 3 135.45 Mbp
30 42 11.19 Mbp 4 134.66 Mbp
40 66 8.80 Mbp 6 130.11 Mbp
50 96 6.97 Mbp 8 125.43 Mbp
60 134 5.60 Mbp 10 103.42 Mbp
70 184 3.97 Mbp 13 77.63 Mbp
80 253 2.81 Mbp 16 69.06 Mbp
90 361 1.53 Mbp 19 60.28 Mbp
100 1248 6.85 Kbp 612 6.85 Kbp
1.000x 1248 2.33 Gbp 612 2.33 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 7 October 2025
mBlaBre2.HiC.hap2.20251007.fasta.gz (570.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 12 16.34 Mbp 1 269.35 Mbp
20 28 11.89 Mbp 2 229.59 Mbp
30 49 9.44 Mbp 3 210.06 Mbp
40 74 7.94 Mbp 5 132.09 Mbp
50 105 6.40 Mbp 6 130.09 Mbp
60 142 5.22 Mbp 8 101.83 Mbp
70 189 3.92 Mbp 11 80.89 Mbp
80 256 2.70 Mbp 14 68.92 Mbp
90 359 1.58 Mbp 17 60.45 Mbp
100 1280 6.63 Kbp 647 6.63 Kbp
1.000x 1280 2.18 Gbp 647 2.18 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 7 October 2025
mBlaBre2.MT.20251007.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mBlaBre2.yml (view)
species: Blarina brevicauda
specimem: mBlaBre2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Blarina_brevicauda/mBlaBre2/assembly_vgp_HiC_2.0/mBlaBre2.HiC.hap1.20251007.fasta.gz
hap2: s3://genomeark/species/Blarina_brevicauda/mBlaBre2/assembly_vgp_HiC_2.0/mBlaBre2.HiC.hap2.20251007.fasta.gz
pretext_hap1: s3://genomeark/species/Blarina_brevicauda/mBlaBre2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mBlaBre2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Blarina_brevicauda/mBlaBre2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mBlaBre2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Blarina_brevicauda/mBlaBre2/assembly_vgp_HiC_2.0/evaluation/merqury/mBlaBre2_png/
pacbio_read_dir: s3://genomeark/species/Blarina_brevicauda/mBlaBre2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Blarina_brevicauda/mBlaBre2/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mBlaBre2 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.