Monodelphis domestica

gray short-tailed opossum

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank mMonDom1: GCA_027887165.1 mMonDom1: GCA_027917375.1
ENA mMonDom1: GCA_027887165.1 mMonDom1: GCA_027917375.1
UCSC Genome Browser mMonDom1: GCA_027887165.1 mMonDom1: GCA_027917375.1

metadata.yaml (view) (edit on github)
species:
  name: Monodelphis domestica
  individuals:
  - short_name: mMonDom1
  short_name: mMonDom
  taxon_id: 13616
  common_name: gray short-tailed opossum
  genome_size: 4592000000
  genome_size_method: GoAT
  order:
    name: Didelphimorphia
  family:
    name: Didelphidae
  project: [ vgp ]
CC BY 2.5 Emma Hill (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mMonDom1 595.09 Gbp 129.59x 1.4 TiB
PacBio HiFi (.fq) mMonDom1 151.07 Gbp 32.90x 121.4 GiB
PacBio HiFi (.bam) mMonDom1 150.30 Gbp 32.73x 519.8 GiB
Bionano mMonDom1 N/A 229.92x 2.0 GiB
Arima mMonDom1 533.40 Gbp 116.16x 256.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.59 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMonDom1 PacBio HiFi (subreads) 595.09 Gbp 129.59x 1.4 TiB
PacBio HiFi (.fq) 151.07 Gbp 32.90x 121.4 GiB
PacBio HiFi (.bam) 150.30 Gbp 32.73x 519.8 GiB
Bionano N/A 229.92x 2.0 GiB
Arima 533.40 Gbp 116.16x 256.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.59 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 3 January 2023
mMonDom1.pri.cur.20230103.fasta.gz (1.0 GiB)

Quality: 1.0 errors/Mb (QV=59.85)

Contigs Scaffolds
NG LG Len LG Len
10 30 11.39 Mbp 0 0.76 Gbp
20 82 7.21 Mbp 1 0.54 Gbp
30 155 5.37 Mbp 2 0.54 Gbp
40 258 3.72 Mbp 2 0.54 Gbp
50 413 2.42 Mbp 3 454.67 Mbp
60 658 1.47 Mbp 5 311.08 Mbp
70 1105 0.68 Mbp 6 293.77 Mbp
80 0 0
90 0 0
100 0 0
0.774x 2268 3.55 Gbp 13 3.59 Gbp
NG based on genome size 4.59 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 5 May 2022
mMonDom1.alt.cur.20220505.fasta.gz (751.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 140 2.18 Mbp 138 2.21 Mbp
20 417 1.30 Mbp 412 1.32 Mbp
30 864 0.83 Mbp 854 0.84 Mbp
40 1565 0.51 Mbp 1549 0.51 Mbp
50 2925 214.16 Kbp 2902 215.19 Kbp
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.570x 8086 2.62 Gbp 8062 2.62 Gbp
NG based on genome size 4.59 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 June 2022
mMonDom1.MT.20220617.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/mMonDom1.yaml (view)
species: Monodelphis_domestica
specimen: mMonDom1
projects:
-vgp
primary:
s3://genomeark/species/Monodelphis_domestica/mMonDom1/assembly_vgp_standard_2.0/https://genomeark.s3.amazonaws.com/species/Monodelphis_domestica/mMonDom1/assembly_vgp_standard_2.0/mMonDom1.pri.asm.20220212.fasta.gz
haplotigs:
s3://genomeark/species/Monodelphis_domestica/mMonDom1/assembly_vgp_standard_2.0/mMonDom1.alt.asm.20211231.fasta.gz
hic_bam:
s3://genomeark/species/Monodelphis_domestica/mMonDom1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mMonDom1_s2.bam
pretext:
s3://genomeark/species/Monodelphis_domestica/mMonDom1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mMonDom1_heatmap.pretext
kmer_spectra_img:
s3://genomeark/species/Monodelphis_domestica/mMonDom1/assembly_vgp_standard_2.0/evaluation/merqury/p/mMonDom1_png/
pipeline:
  - hifiasm (0.15.4+galaxy)
  - purge_dups (1.2.5+galaxy3)
  - bionano_solve (3.6.1+galaxy2)
  - salsa (2.3+galaxy0)
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.