Rousettus madagascariensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mRouMad1 155.58 Gbp N/A 74.8 GiB
PacBio HiFi (.bam) mRouMad1 161.50 Gbp N/A 524.6 GiB
Arima mRouMad1 322.95 Gbp N/A 175.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mRouMad1 PacBio HiFi (.fq) 155.58 Gbp N/A 74.8 GiB
PacBio HiFi (.bam) 161.50 Gbp N/A 524.6 GiB
Arima 322.95 Gbp N/A 175.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 10 October 2025
mRouMad1.HiC.hap1.20251010.fasta.gz (492.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 151.73 Mbp 1 187.27 Mbp
20 3 123.37 Mbp 3 176.88 Mbp
30 4 120.66 Mbp 4 162.78 Mbp
40 6 106.48 Mbp 5 123.37 Mbp
50 8 97.81 Mbp 6 116.58 Mbp
60 10 61.73 Mbp 8 115.14 Mbp
70 13 54.85 Mbp 10 101.06 Mbp
80 17 40.54 Mbp 11 97.81 Mbp
90 23 26.67 Mbp 13 82.19 Mbp
100 110 6.81 Kbp 81 6.81 Kbp
1.000x 110 1.85 Gbp 81 1.85 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 10 October 2025
mRouMad1.HiC.hap2.20251010.fasta.gz (519.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 120.53 Mbp 1 357.43 Mbp
20 3 114.47 Mbp 2 186.54 Mbp
30 5 92.39 Mbp 3 177.77 Mbp
40 7 82.67 Mbp 4 177.20 Mbp
50 10 74.26 Mbp 5 163.18 Mbp
60 13 57.24 Mbp 6 124.40 Mbp
70 17 45.70 Mbp 8 117.11 Mbp
80 21 33.55 Mbp 10 114.16 Mbp
90 29 23.27 Mbp 12 97.67 Mbp
100 105 16.71 Kbp 68 16.71 Kbp
1.000x 105 1.95 Gbp 68 1.95 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 October 2025
mRouMad1.MT.20251010.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mRouMad1.yml (view)
species: Rousettus madagascariensis
specimem: mRouMad1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Rousettus_madagascariensis/mRouMad1/assembly_vgp_HiC_2.0/mRouMad1.HiC.hap1.20251010.fasta.gz
hap2: s3://genomeark/species/Rousettus_madagascariensis/mRouMad1/assembly_vgp_HiC_2.0/mRouMad1.HiC.hap2.20251010.fasta.gz
pretext_hap1: s3://genomeark/species/Rousettus_madagascariensis/mRouMad1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mRouMad1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Rousettus_madagascariensis/mRouMad1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mRouMad1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Rousettus_madagascariensis/mRouMad1/assembly_vgp_HiC_2.0/evaluation/merqury/mRouMad1_png/
pacbio_read_dir: s3://genomeark/species/Rousettus_madagascariensis/mRouMad1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Rousettus_madagascariensis/mRouMad1/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 mRouMad1 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.