Sigmodon hispidus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mSigHis2 221.08 Gbp N/A 98.6 GiB
PacBio HiFi (.bam) mSigHis2 223.19 Gbp N/A 722.7 GiB
Arima mSigHis2 333.88 Gbp N/A 175.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 November 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mSigHis2 PacBio HiFi (.fq) 221.08 Gbp N/A 98.6 GiB
PacBio HiFi (.bam) 223.19 Gbp N/A 722.7 GiB
Arima 333.88 Gbp N/A 175.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 November 2025.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 8 January 2025
mSigHis2.HiC.hap1.20250108.fasta.gz (707.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 138.12 Mbp 2 196.78 Mbp
20 5 108.12 Mbp 3 191.80 Mbp
30 8 78.39 Mbp 4 191.62 Mbp
40 12 63.19 Mbp 6 148.53 Mbp
50 16 49.52 Mbp 8 127.51 Mbp
60 23 37.68 Mbp 10 117.90 Mbp
70 31 30.26 Mbp 13 83.23 Mbp
80 41 23.20 Mbp 16 70.62 Mbp
90 56 13.21 Mbp 20 65.77 Mbp
100 259 16.71 Kbp 160 16.71 Kbp
1.000x 259 2.70 Gbp 160 2.70 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 8 January 2025
mSigHis2.HiC.hap2.20250108.fasta.gz (711.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 112.39 Mbp 2 202.77 Mbp
20 6 78.50 Mbp 3 188.03 Mbp
30 9 62.14 Mbp 5 160.53 Mbp
40 14 56.83 Mbp 6 148.49 Mbp
50 20 43.08 Mbp 8 127.64 Mbp
60 28 33.22 Mbp 11 115.66 Mbp
70 37 23.80 Mbp 13 83.08 Mbp
80 50 18.37 Mbp 17 67.84 Mbp
90 70 9.84 Mbp 21 61.66 Mbp
100 295 21.88 Kbp 160 21.88 Kbp
1.000x 295 2.75 Gbp 160 2.75 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 8 January 2026
mSigHis2.MT.20260108.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mSigHis2.yml (view)
species: Sigmodon hispidus
specimem: mSigHis2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Sigmodon_hispidus/mSigHis2/assembly_vgp_HiC_2.0/mSigHis2.HiC.hap1.20250108.fasta.gz
hap2: s3://genomeark/species/Sigmodon_hispidus/mSigHis2/assembly_vgp_HiC_2.0/mSigHis2.HiC.hap2.20250108.fasta.gz
pretext_hap1: s3://genomeark/species/Sigmodon_hispidus/mSigHis2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mSigHis2_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Sigmodon_hispidus/mSigHis2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mSigHis2_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Sigmodon_hispidus/mSigHis2/assembly_vgp_HiC_2.0/evaluation/merqury/mSigHis2_png/
pacbio_read_dir: s3://genomeark/species/Sigmodon_hispidus/mSigHis2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Sigmodon_hispidus/mSigHis2/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.6)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.2) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mSigHis2 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.