Peromyscus gossypinus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mPerGos1 144.32 Gbp N/A 70.7 GiB
PacBio HiFi (.bam) mPerGos1 143.67 Gbp N/A 574.2 GiB
Arima mPerGos1 212.56 Gbp N/A 115.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPerGos1 PacBio HiFi (.fq) 144.32 Gbp N/A 70.7 GiB
PacBio HiFi (.bam) 143.67 Gbp N/A 574.2 GiB
Arima 212.56 Gbp N/A 115.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 27 June 2024
mPerGos1.HiC.hap1.20240627.fasta.gz (766.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 92.65 Mbp 2 177.19 Mbp
20 6 82.79 Mbp 3 171.28 Mbp
30 10 75.01 Mbp 5 143.27 Mbp
40 14 72.27 Mbp 7 141.79 Mbp
50 17 68.69 Mbp 10 103.58 Mbp
60 23 44.26 Mbp 13 90.48 Mbp
70 29 36.89 Mbp 16 81.31 Mbp
80 40 22.24 Mbp 20 69.64 Mbp
90 61 8.44 Mbp 24 62.54 Mbp
100 569 15.66 Kbp 510 15.66 Kbp
1.000x 569 2.82 Gbp 510 2.82 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 27 June 2024
mPerGos1.HiC.hap2.20240627.fasta.gz (712.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 103.46 Mbp 2 174.49 Mbp
20 5 90.82 Mbp 3 170.71 Mbp
30 8 79.58 Mbp 5 141.92 Mbp
40 12 66.64 Mbp 7 122.62 Mbp
50 16 55.90 Mbp 9 103.46 Mbp
60 21 45.19 Mbp 11 93.19 Mbp
70 27 40.81 Mbp 14 84.63 Mbp
80 34 31.21 Mbp 18 70.44 Mbp
90 44 16.21 Mbp 22 57.41 Mbp
100 277 14.21 Kbp 230 14.21 Kbp
1.000x 277 2.55 Gbp 230 2.55 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 27 June 2024
mPerGos1.MT.20240627.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mPerGos1.yml (view)
species: Peromyscus gossypinus
specimen: mPerGos1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Peromyscus_gossypinus/mPerGos1/assembly_vgp_HiC_2.0/mPerGos1.HiC.hap1.20240627.fasta.gz
hap2: s3://genomeark/species/Peromyscus_gossypinus/mPerGos1/assembly_vgp_HiC_2.0/mPerGos1.HiC.hap2.20240627.fasta.gz
pretext_hap1: s3://genomeark/species/Peromyscus_gossypinus/mPerGos1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mPerGos1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Peromyscus_gossypinus/mPerGos1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mPerGos1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Peromyscus_gossypinus/mPerGos1/assembly_vgp_HiC_2.0/evaluation/merqury/mPerGos1_png/
mito: s3://genomeark/species/Peromyscus_gossypinus/mPerGos1/assembly_MT_rockefeller/mPerGos1.MT.20240627.fasta.gz
pacbio_read_dir: s3://genomeark/species/Peromyscus_gossypinus/mPerGos1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Peromyscus_gossypinus/mPerGos1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy1)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mPerGos1, resulting in two complete haplotypes. The HiC prep kit used was Arima, so the HiC reads require trimming 5 bp off the 5' end. The assembly was performed on the Rockefeller University VGL instance. 
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.