Monophyllus redmani

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mMonRed1 91.74 Gbp N/A 79.1 GiB
PacBio HiFi (.bam) mMonRed1 91.18 Gbp N/A 327.3 GiB
Arima mMonRed1 288.71 Gbp N/A 158.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 April 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMonRed1 PacBio HiFi (.fq) 91.74 Gbp N/A 79.1 GiB
PacBio HiFi (.bam) 91.18 Gbp N/A 327.3 GiB
Arima 288.71 Gbp N/A 158.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 April 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 27 May 2026
mMonRed1.HiC.hap1.20260527.fasta.gz (584.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 173.63 Mbp 1 219.16 Mbp
20 3 146.90 Mbp 2 212.29 Mbp
30 4 124.94 Mbp 4 203.36 Mbp
40 6 114.51 Mbp 5 175.89 Mbp
50 8 96.62 Mbp 6 166.85 Mbp
60 11 69.13 Mbp 7 142.14 Mbp
70 15 58.77 Mbp 9 115.12 Mbp
80 18 48.85 Mbp 11 107.80 Mbp
90 24 32.39 Mbp 13 69.13 Mbp
100 66 29.33 Kbp 37 29.33 Kbp
1.000x 66 2.15 Gbp 37 2.15 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 27 May 2026
mMonRed1.HiC.hap2.20260527.fasta.gz (555.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 219.34 Mbp 1 234.15 Mbp
20 2 211.35 Mbp 2 219.34 Mbp
30 3 210.13 Mbp 3 212.54 Mbp
40 5 139.98 Mbp 4 210.13 Mbp
50 6 132.66 Mbp 5 176.23 Mbp
60 8 101.80 Mbp 7 142.49 Mbp
70 10 94.18 Mbp 8 132.66 Mbp
80 12 75.67 Mbp 10 107.95 Mbp
90 15 55.74 Mbp 12 69.38 Mbp
100 47 16.80 Kbp 32 16.80 Kbp
1.000x 47 2.04 Gbp 32 2.04 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 26 May 2026
mMonRed1.MT.20260526.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mMonRed1.yml (view)
species: Monophyllus redmani
specimen: mMonRed1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Monophyllus_redmani/mMonRed1/assembly_vgp_HiC_2.0/mMonRed1.HiC.hap1.20260527.fasta.gz
hap2: s3://genomeark/species/Monophyllus_redmani/mMonRed1/assembly_vgp_HiC_2.0/mMonRed1.HiC.hap2.20260527.fasta.gz
pretext_hap1: s3://genomeark/species/Monophyllus_redmani/mMonRed1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mMonRed1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Monophyllus_redmani/mMonRed1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mMonRed1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Monophyllus_redmani/mMonRed1/assembly_vgp_HiC_2.0/evaluation/merqury/mMonRed1_png/
pacbio_read_dir: s3://genomeark/species/Monophyllus_redmani/mMonRed1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Monophyllus_redmani/mMonRed1/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)
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10
  - VGP9 decontamination workflow (v1.3)
  - Pre-curation workflow (v2.4) with mapq=10, keep HiC duplicates and generate high-resolution map
notes: This was a Hifiasm-HiC assembly of mMonRed1 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.