Castor canadensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mCasCan1 188.01 Gbp N/A 84.0 GiB
PacBio HiFi (.bam) mCasCan1 191.77 Gbp N/A 611.9 GiB
Arima mCasCan1 263.73 Gbp N/A 143.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 October 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mCasCan1 PacBio HiFi (.fq) 188.01 Gbp N/A 84.0 GiB
PacBio HiFi (.bam) 191.77 Gbp N/A 611.9 GiB
Arima 263.73 Gbp N/A 143.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 October 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 2 December 2024
mCasCan1.hap1.cur.20241202.fasta.gz (797.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 145.26 Mbp 2 202.87 Mbp
20 5 87.07 Mbp 3 199.90 Mbp
30 8 83.10 Mbp 5 182.35 Mbp
40 12 69.18 Mbp 6 177.51 Mbp
50 16 59.38 Mbp 8 158.97 Mbp
60 21 51.05 Mbp 10 148.55 Mbp
70 29 29.09 Mbp 12 143.27 Mbp
80 40 23.25 Mbp 14 127.04 Mbp
90 59 9.12 Mbp 16 102.61 Mbp
100 771 11.45 Kbp 590 11.45 Kbp
1.000x 771 2.83 Gbp 590 2.83 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 2 December 2024
mCasCan1.hap2.cur.20241202.fasta.gz (783.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 90.63 Mbp 2 200.42 Mbp
20 7 83.69 Mbp 3 193.56 Mbp
30 10 70.69 Mbp 5 181.09 Mbp
40 15 54.03 Mbp 6 174.12 Mbp
50 20 49.96 Mbp 8 158.54 Mbp
60 26 38.97 Mbp 10 147.34 Mbp
70 35 26.57 Mbp 12 142.49 Mbp
80 48 17.19 Mbp 14 128.65 Mbp
90 69 7.96 Mbp 16 101.01 Mbp
100 432 15.89 Kbp 238 15.89 Kbp
1.000x 432 2.77 Gbp 238 2.77 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 18 October 2024
mCasCan1.MT.20241018.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mCasCan1.yml.yaml (view)
species: Castor canadensis
specimen: mCasCan1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Castor_canadensis/mCasCan1/assembly_vgp_HiC_2.0/evaluation/mCasCan1.HiC.hap1.20241018.fasta.gz
hap2: s3://genomeark/species/Castor_canadensis/mCasCan1/assembly_vgp_HiC_2.0/evaluation/mCasCan1.HiC.hap2.20241018.fasta.gz
pretext_hap1: s3://genomeark/species/Castor_canadensis/mCasCan1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mCasCan1_hap1__s1_heatmap.pretext
pretext_hap2: s3://genomeark/species/Castor_canadensis/mCasCan1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mCasCan1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Castor_canadensis/mCasCan1/assembly_vgp_HiC_2.0/evaluation/merqury/mCasCan1_png
pacbio_read_dir: s3://genomeark/species/Castor_canadensis/mCasCan1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Castor_canadensis/mCasCan1/genomic_data/arima/
mito: s3://genomeark/species/species/Castor_canadensis/mCasCan1/assembly_MT_rockefeller/mCasCan1.MT.20241018.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mCasCan1, 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 is a VGP Phase 1 species we are submitting for dual curation.
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.