Peromyscus truei

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mPerTru1 217.98 Gbp N/A 98.7 GiB
PacBio HiFi (.bam) mPerTru1 220.71 Gbp N/A 722.3 GiB
Arima mPerTru1 612.64 Gbp N/A 320.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 22 October 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mPerTru1 PacBio HiFi (.fq) 217.98 Gbp N/A 98.7 GiB
PacBio HiFi (.bam) 220.71 Gbp N/A 722.3 GiB
Arima 612.64 Gbp N/A 320.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 22 October 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 22 October 2025
mPerTru1.HiC.hap1.20251022.fasta.gz (656.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 142.25 Mbp 1 326.06 Mbp
20 4 127.57 Mbp 2 268.21 Mbp
30 6 96.99 Mbp 3 264.67 Mbp
40 9 83.77 Mbp 4 172.90 Mbp
50 12 72.80 Mbp 6 127.57 Mbp
60 16 66.87 Mbp 8 100.99 Mbp
70 20 53.57 Mbp 11 88.71 Mbp
80 26 34.42 Mbp 14 70.97 Mbp
90 34 21.55 Mbp 18 66.87 Mbp
100 294 13.34 Kbp 227 13.34 Kbp
1.000x 294 2.47 Gbp 227 2.47 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 22 October 2025
mPerTru1.HiC.hap2.20251022.fasta.gz (709.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 159.48 Mbp 1 328.09 Mbp
20 4 124.08 Mbp 2 209.51 Mbp
30 6 113.77 Mbp 4 172.73 Mbp
40 9 96.33 Mbp 6 138.31 Mbp
50 12 80.98 Mbp 8 122.68 Mbp
60 15 72.28 Mbp 10 100.72 Mbp
70 19 63.96 Mbp 13 88.01 Mbp
80 25 41.05 Mbp 16 71.58 Mbp
90 34 20.07 Mbp 20 66.26 Mbp
100 177 20.83 Kbp 118 20.83 Kbp
1.000x 177 2.67 Gbp 118 2.67 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 22 October 2025
mPerTru1.MT.20251022.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mPerTru1.yml (view)
species: Peromyscus truei
specimem: mPerTru1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Peromyscus_truei/mPerTru1/assembly_vgp_HiC_2.0/mPerTru1.HiC.hap1.20251022.fasta.gz
hap2: s3://genomeark/species/Peromyscus_truei/mPerTru1/assembly_vgp_HiC_2.0/mPerTru1.HiC.hap2.20251022.fasta.gz
pretext_hap1: s3://genomeark/species/Peromyscus_truei/mPerTru1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mPerTru1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Peromyscus_truei/mPerTru1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mPerTru1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Peromyscus_truei/mPerTru1/assembly_vgp_HiC_2.0/evaluation/merqury/mPerTru1_png/
pacbio_read_dir: s3://genomeark/species/Peromyscus_truei/mPerTru1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Peromyscus_truei/mPerTru1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.1) with default mapq=10
  - VGP9 decontamination workflow (v1.1) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mPerTru1 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.