Sorex araneus

European shrew

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank mSorAra2: GCA_027595985.1 mSorAra2: GCA_027595995.1
ENA mSorAra2: GCA_027595985.1 mSorAra2: GCA_027595995.1
UCSC Genome Browser mSorAra2: GCA_027595985.1 mSorAra2: GCA_027595995.1

metadata.yaml (view) (edit on github)
species:
  name: Sorex araneus
  individuals:
  - short_name: mSorAra1
  short_name: mSorAra
  taxon_id: 42254
  common_name: European shrew
  genome_size: 2846000000
  genome_size_method: GoAT
  order:
    name: Eulipotyphla
  family:
    name: Soricidae
  project: [ vgp ]
CC BY-NC-ND 2.0 Hanna Knutsson (flickr), modified with permission
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mSorAra1 684.79 Gbp 240.61x 1.4 TiB
PacBio HiFi (.fq) mSorAra1 99.93 Gbp 35.11x 75.6 GiB
PacBio HiFi (.bam) mSorAra1 100.40 Gbp 35.28x 250.9 GiB
Bionano mSorAra1 N/A 471.82x 2.5 GiB
Arima mSorAra1 294.87 Gbp 103.61x 137.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.85 Gbp.
Last upload on 4 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mSorAra1 PacBio HiFi (subreads) 684.79 Gbp 240.61x 1.4 TiB
PacBio HiFi (.fq) 99.93 Gbp 35.11x 75.6 GiB
PacBio HiFi (.bam) 100.40 Gbp 35.28x 250.9 GiB
Bionano N/A 471.82x 2.5 GiB
Arima 294.87 Gbp 103.61x 137.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.85 Gbp.
Last upload on 4 May 2022.
Assemblies
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 June 2022
mSorAra1.MT.20220617.fasta.gz (5.0 KiB)

Quality: not computed
Individual 2 Primary Assembly
Version assembly_curated from 7 July 2022
mSorAra2.pri.cur.20220707.fasta.gz (692.5 MiB)

Quality: 1.0 errors/Mb (QV=59.87)

Contigs Scaffolds
NG LG Len LG Len
10 23 8.84 Mbp 0 452.70 Mbp
20 60 6.69 Mbp 1 381.07 Mbp
30 107 5.40 Mbp 2 374.36 Mbp
40 166 4.19 Mbp 2 374.36 Mbp
50 243 3.25 Mbp 3 239.58 Mbp
60 347 2.26 Mbp 5 216.57 Mbp
70 508 1.35 Mbp 6 169.03 Mbp
80 836 491.18 Kbp 10 67.95 Mbp
90 0 0
100 0 0
0.841x 1492 2.39 Gbp 65 2.41 Gbp
NG based on genome size 2.85 Gbp.
Individual 2 Alternate Assembly
Version assembly_curated from 7 July 2022
mSorAra2.alt.cur.20220707.fasta.gz (671.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 89 2.34 Mbp 89 2.34 Mbp
20 231 1.72 Mbp 231 1.72 Mbp
30 423 1.30 Mbp 423 1.30 Mbp
40 681 0.95 Mbp 681 0.95 Mbp
50 1025 0.72 Mbp 1025 0.72 Mbp
60 1496 0.51 Mbp 1496 0.51 Mbp
70 2232 292.05 Kbp 2232 292.05 Kbp
80 4176 48.61 Kbp 4176 48.61 Kbp
90 0 0
100 0 0
0.815x 5699 2.32 Gbp 5699 2.32 Gbp
NG based on genome size 2.85 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/mSorAra1.yaml (view)
species: Sorex araneus
specimen: mSorAra1
projects:
  - vgp
primary: s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/mSorAra1.pri.asm.20211103.fasta.gz
haplotigs: s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/mSorAra1.alt.asm.20211103.fasta.gz
hic_bam: s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mSorAra1_s2.bam
pretext: s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mSorAra1_s2.pretext
kmer_spectra_img: s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/evaluation/merqury/p/mSorAra1_images/
pipeline:
  - hifiasm (0.15.4+galaxy0)
  - purge_dups (1.2.5+galaxy3)
  - bionano scaffold (3.6.1+galaxy2)
  - salsa (2.3+galaxy1)
assembly_vgp_standard_2.0/mSorAra2.yaml (view)
species: Sorex araneus
specimen: mSorAra2
projects:
  - vgp
primary: s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/mSorAra2.pri.asm.20211103.fasta.gz
haplotigs: s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/mSorAra2.alt.asm.20211103.fasta.gz
hic_bam: s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mSorAra1_s2.bam
pretext: s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mSorAra1_s2.pretext
kmer_spectra_img: s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/evaluation/merqury/p/mSorAra1_images/
pipeline:
  - hifiasm (0.15.4+galaxy0)
  - purge_dups (1.2.5+galaxy3)
  - bionano scaffold (3.6.1+galaxy2)
  - salsa (2.3+galaxy1)
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.