Aplodontia rufa

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mAplRuf1 240.29 Gbp N/A 103.8 GiB
PacBio HiFi (.bam) mAplRuf1 220.73 Gbp N/A 713.5 GiB
Arima mAplRuf1 226.84 Gbp N/A 117.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 5 August 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mAplRuf1 PacBio HiFi (.fq) 240.29 Gbp N/A 103.8 GiB
PacBio HiFi (.bam) 220.73 Gbp N/A 713.5 GiB
Arima 226.84 Gbp N/A 117.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 5 August 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 11 September 2026
mAplRuf1.hap1.cur.20260911.fasta.gz (877.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 177.73 Mbp 2 228.33 Mbp
20 4 121.35 Mbp 4 172.63 Mbp
30 7 103.68 Mbp 5 171.39 Mbp
40 11 80.02 Mbp 7 167.33 Mbp
50 15 70.53 Mbp 10 135.75 Mbp
60 21 46.35 Mbp 12 122.95 Mbp
70 28 33.31 Mbp 15 105.38 Mbp
80 43 14.38 Mbp 18 86.84 Mbp
90 86 4.15 Mbp 23 65.30 Mbp
100 702 527 bp 502 5.75 Kbp
1.000x 702 3.26 Gbp 502 3.26 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 11 September 2026
mAplRuf1.hap2.cur.20260911.fasta.gz (755.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 172.99 Mbp 2 227.27 Mbp
20 5 118.90 Mbp 3 191.98 Mbp
30 8 107.67 Mbp 5 172.35 Mbp
40 11 99.10 Mbp 7 162.82 Mbp
50 14 90.52 Mbp 9 138.54 Mbp
60 18 55.27 Mbp 12 118.74 Mbp
70 27 27.45 Mbp 15 94.58 Mbp
80 45 9.79 Mbp 19 74.09 Mbp
90 111 2.79 Mbp 26 11.77 Mbp
100 701 3.08 Kbp 534 13.41 Kbp
1.000x 701 3.20 Gbp 534 3.20 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 18 August 2026
mAplRuf1.MT.20260818.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mAplRuf1.yml (view)
species: Aplodontia rufa
specimen: mAplRuf1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Aplodontia_rufa/mAplRuf1/assembly_vgp_HiC_2.0/mAplRuf1.HiC.hap1.20260820.fasta.gz
hap2: s3://genomeark/species/Aplodontia_rufa/mAplRuf1/assembly_vgp_HiC_2.0/mAplRuf1.HiC.hap2.20260820.fasta.gz
pretext_hap1: s3://genomeark/species/Aplodontia_rufa/mAplRuf1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mAplRuf1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Aplodontia_rufa/mAplRuf1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mAplRuf1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Aplodontia_rufa/mAplRuf1/assembly_vgp_HiC_2.0/evaluation/merqury/mAplRuf1_png/
pacbio_read_dir: s3://genomeark/species/Aplodontia_rufa/mAplRuf1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Aplodontia_rufa/mAplRuf1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.9)
  - VGP4 HiFi HiC assembly workflow (v0.6). Rerun compleasm (v0.2.9+galaxy0) manually
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10. Rerun compleasm (v0.2.9+galaxy0) manually
  - VGP9 decontamination workflow (v1.3)
  - Pre-curation workflow (v3.0 2026526 update) with mapq=10, remove HiC duplicates and generate ultra-high-resolution map
notes: This was a Hifiasm-HiC assembly of mAplRuf1 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.