Reithrodontomys humulis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mReiHum1 163.24 Gbp N/A 72.3 GiB
PacBio HiFi (.bam) mReiHum1 169.12 Gbp N/A 545.6 GiB
Arima mReiHum1 257.09 Gbp N/A 138.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 July 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mReiHum1 PacBio HiFi (.fq) 163.24 Gbp N/A 72.3 GiB
PacBio HiFi (.bam) 169.12 Gbp N/A 545.6 GiB
Arima 257.09 Gbp N/A 138.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 July 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 15 October 2025
mReiHum1.HiC.hap1.20251015.fasta.gz (863.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 85.91 Mbp 3 174.44 Mbp
20 9 58.10 Mbp 5 168.20 Mbp
30 17 46.68 Mbp 7 155.65 Mbp
40 26 37.04 Mbp 10 122.91 Mbp
50 37 29.19 Mbp 13 112.76 Mbp
60 51 23.23 Mbp 16 106.00 Mbp
70 70 15.70 Mbp 21 71.23 Mbp
80 100 10.00 Mbp 29 27.15 Mbp
90 154 4.61 Mbp 61 6.29 Mbp
100 655 18.58 Kbp 528 18.58 Kbp
1.000x 655 3.72 Gbp 528 3.72 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 15 October 2025
mReiHum1.HiC.hap2.20251015.fasta.gz (750.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 100.70 Mbp 2 177.41 Mbp
20 8 63.60 Mbp 4 167.45 Mbp
30 13 54.20 Mbp 6 150.43 Mbp
40 19 46.21 Mbp 8 128.75 Mbp
50 28 33.58 Mbp 11 113.55 Mbp
60 39 24.93 Mbp 14 98.29 Mbp
70 54 17.40 Mbp 17 75.89 Mbp
80 78 9.23 Mbp 22 53.90 Mbp
90 126 4.10 Mbp 42 5.88 Mbp
100 653 20.80 Kbp 527 20.80 Kbp
1.000x 653 3.12 Gbp 527 3.12 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 October 2025
mReiHum1.MT.20251015.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mReiHum1.yml (view)
species: Reithrodontomys humulis
specimem: mReiHum1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Reithrodontomys_humulis/mReiHum1/assembly_vgp_HiC_2.0/mReiHum1.HiC.hap1.20251015.fasta.gz
hap2: s3://genomeark/species/Reithrodontomys_humulis/mReiHum1/assembly_vgp_HiC_2.0/mReiHum1.HiC.hap2.20251015.fasta.gz
pretext_hap1: s3://genomeark/species/Reithrodontomys_humulis/mReiHum1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mReiHum1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Reithrodontomys_humulis/mReiHum1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mReiHum1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Reithrodontomys_humulis/mReiHum1/assembly_vgp_HiC_2.0/evaluation/merqury/mReiHum1_png/
pacbio_read_dir: s3://genomeark/species/Reithrodontomys_humulis/mReiHum1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Reithrodontomys_humulis/mReiHum1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mReiHum1 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.