Erethizon dorsatum

North American porcupine

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank mEreDor1: GCA_028451465.1 mEreDor1: GCA_028500835.1
ENA mEreDor1: GCA_028451465.1 mEreDor1: GCA_028500835.1
UCSC Genome Browser mEreDor1: GCA_028451465.1 mEreDor1: GCA_028500835.1

metadata.yaml (view) (edit on github)
species:
  common_name: North American porcupine
  family:
    name: Erethizontidae
  genome_size: 2900000000
  genome_size_method: null
  individuals:
  - short_name: mEreDor1
  name: Erethizon dorsatum
  order:
    name: Rodentia
  short_name: mEreDor
  taxon_id: 34844
  project: [ vgp ]
CC BY-NC-SA 2.0 Arthur Chapman (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR mEreDor1 334.12 Gbp 115.21x 591.9 GiB
10x mEreDor1 235.27 Gbp 81.13x 119.9 GiB
Arima mEreDor1 337.66 Gbp 116.44x 215.4 GiB
Illumina mEreDor1 326.51 Gbp 112.59x 160.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.90 Gbp.
Last upload on 27 July 2021.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mEreDor1 PacBio CLR 334.12 Gbp 115.21x 591.9 GiB
10x 235.27 Gbp 81.13x 119.9 GiB
Arima 337.66 Gbp 116.44x 215.4 GiB
Illumina 326.51 Gbp 112.59x 160.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.90 Gbp.
Last upload on 27 July 2021.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 20 January 2023
mEreDor1.pri.cur.20230120.fasta.gz (708.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 57.92 Mbp 1 164.61 Mbp
20 10 40.36 Mbp 3 151.49 Mbp
30 19 27.91 Mbp 5 140.56 Mbp
40 31 19.68 Mbp 7 132.85 Mbp
50 48 14.91 Mbp 9 127.61 Mbp
60 70 11.06 Mbp 12 117.54 Mbp
70 105 6.85 Mbp 14 109.04 Mbp
80 167 2.96 Mbp 18 52.51 Mbp
90 0 0
100 0 0
0.839x 392 2.43 Gbp 115 2.43 Gbp
NG based on genome size 2.90 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 20 January 2023
mEreDor1.alt.cur.20230120.fasta.gz (568.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 146 1.52 Mbp 146 1.52 Mbp
20 383 0.99 Mbp 383 0.99 Mbp
30 731 0.71 Mbp 731 0.71 Mbp
40 1225 490.72 Kbp 1224 490.91 Kbp
50 1954 321.36 Kbp 1953 321.46 Kbp
60 3143 180.77 Kbp 3142 180.77 Kbp
70 0 0
80 0 0
90 0 0
100 0 0
0.672x 5183 1.95 Gbp 5180 1.95 Gbp
NG based on genome size 2.90 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 27 July 2021
mEreDor1.MT.20210727.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_1.7/mEreDor1.yaml (view)
species: Erethizon dorsatum
specimen: mEreDor1
projects:
  - vgp
primary: s3://genomeark/species/Erethizon_dorsatum/mEreDor1/assembly_vgp_standard_1.7/mEreDor1.pri.asm.20210907.fasta.gz
haplotigs: s3://genomeark/species/Erethizon_dorsatum/mEreDor1/assembly_vgp_standard_1.7/mEreDor1.alt.asm.20210907.fasta.gz
mito: s3://genomeark/species/Erethizon_dorsatum/mEreDor1/assembly_MT_rockefeller/mEreDor1.MT.20210727.fasta.gz
hic_bam: s3://genomeark/species/Erethizon_dorsatum/mEreDor1/assembly_vgp_standard_1.7/evaluation/pretext/pri/mEreDor1.pri.asm.20210907.bam
pretext: s3://genomeark/species/Erethizon_dorsatum/mEreDor1/assembly_vgp_standard_1.7/evaluation/pretext/pri/mEreDor1.pri.asm.20210907.pretext
kmer_spectra_img: s3://genomeark/species/Erethizon_dorsatum/mEreDor1/assembly_vgp_standard_1.7/evaluation/merqury/
pipeline:
  - falcon-kit (1.8.1)
  - falcon_unzip (1.3.7)
  - purge_dups (1.2.5)
  - scaff10x (2.0.3)
  - salsa (2.2)
  - gcpp (2.0.2)
  - merfin (1.0)
  - freebayes (1.3.1)
  
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.