Megophrys montana

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aMegMon1 155.49 Gbp N/A 69.6 GiB
PacBio HiFi (.bam) aMegMon1 138.80 Gbp N/A 380.4 GiB
Arima aMegMon1 168.39 Gbp N/A 90.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 9 June 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aMegMon1 PacBio HiFi (.fq) 155.49 Gbp N/A 69.6 GiB
PacBio HiFi (.bam) 138.80 Gbp N/A 380.4 GiB
Arima 168.39 Gbp N/A 90.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 9 June 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 25 June 2026
aMegMon1.hap1.cur.20260625.fasta.gz (701.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 35.32 Mbp 1 445.70 Mbp
20 16 22.49 Mbp 2 359.09 Mbp
30 28 18.17 Mbp 2 359.09 Mbp
40 45 14.28 Mbp 3 302.77 Mbp
50 65 11.31 Mbp 4 297.70 Mbp
60 90 8.97 Mbp 5 255.33 Mbp
70 123 6.72 Mbp 6 126.59 Mbp
80 167 4.72 Mbp 9 112.85 Mbp
90 244 2.27 Mbp 11 97.08 Mbp
100 701 11.78 Kbp 182 12.99 Kbp
1.000x 701 2.53 Gbp 182 2.53 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 25 June 2026
aMegMon1.hap2.cur.20260625.fasta.gz (636.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 34.50 Mbp 1 442.14 Mbp
20 15 26.24 Mbp 2 360.88 Mbp
30 26 20.90 Mbp 2 360.88 Mbp
40 40 16.11 Mbp 3 299.94 Mbp
50 56 13.49 Mbp 4 293.76 Mbp
60 77 11.21 Mbp 5 251.68 Mbp
70 105 7.33 Mbp 6 123.57 Mbp
80 150 4.46 Mbp 8 117.55 Mbp
90 224 2.42 Mbp 11 94.70 Mbp
100 607 8.50 Kbp 104 13.48 Kbp
1.000x 607 2.49 Gbp 104 2.49 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 16 June 2026
aMegMon1.MT.20260616.fasta.gz (6.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/aMegMon1.yml (view)
species: Megophrys montana
specimen: aMegMon1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Megophrys_montana/aMegMon1/assembly_vgp_HiC_2.0/aMegMon1.HiC.hap1.20260615.fasta.gz
hap2: s3://genomeark/species/Megophrys_montana/aMegMon1/assembly_vgp_HiC_2.0/aMegMon1.HiC.hap2.20260615.fasta.gz
pretext_hap1: s3://genomeark/species/Megophrys_montana/aMegMon1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/aMegMon1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Megophrys_montana/aMegMon1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/aMegMon1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Megophrys_montana/aMegMon1/assembly_vgp_HiC_2.0/evaluation/merqury/aMegMon1_png/
pacbio_read_dir: s3://genomeark/species/Megophrys_montana/aMegMon1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Megophrys_montana/aMegMon1/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 (v20260526 update) with mapq=10, keep HiC duplicates and generate standard resolution map
notes: This was a Hifiasm-HiC assembly of aMegMon1 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. The QC step compleasm was run locally (v0.2.6). 
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.