Mantella aurantiaca

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) aManAur1 570.46 Gbp N/A 1.0 TiB
PacBio HiFi (.fq) aManAur1 89.25 Gbp N/A 44.3 GiB
PacBio HiFi (.bam) aManAur1 441.74 Gbp N/A 478.8 GiB
Arima aManAur1 309.67 Gbp N/A 166.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 November 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aManAur1 PacBio HiFi (subreads) 570.46 Gbp N/A 1.0 TiB
PacBio HiFi (.fq) 89.25 Gbp N/A 44.3 GiB
PacBio HiFi (.bam) 441.74 Gbp N/A 478.8 GiB
Arima 309.67 Gbp N/A 166.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 November 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 18 February 2025
aManAur1.hap1.cur.20250218.fasta.gz (819.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 39 6.85 Mbp 1 0.51 Gbp
20 97 5.10 Mbp 2 415.76 Mbp
30 173 3.80 Mbp 3 380.75 Mbp
40 272 2.94 Mbp 4 365.22 Mbp
50 401 2.27 Mbp 5 333.09 Mbp
60 578 1.59 Mbp 6 183.27 Mbp
70 840 1.02 Mbp 7 171.32 Mbp
80 1278 0.57 Mbp 9 165.85 Mbp
90 2170 239.44 Kbp 12 106.81 Mbp
100 7225 1 bp 3087 2.28 Kbp
1.000x 7225 3.34 Gbp 3087 3.34 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 6 February 2025
aManAur1.hap2.cur.20250206.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 33 7.74 Mbp 1 499.05 Mbp
20 85 5.50 Mbp 2 416.97 Mbp
30 157 4.09 Mbp 3 378.96 Mbp
40 251 3.06 Mbp 4 372.18 Mbp
50 377 2.24 Mbp 4 372.18 Mbp
60 551 1.59 Mbp 5 329.36 Mbp
70 808 1.05 Mbp 7 166.91 Mbp
80 1224 0.60 Mbp 9 146.99 Mbp
90 2076 251.71 Kbp 12 107.00 Mbp
100 6532 117 bp 2611 3.41 Kbp
1.000x 6532 3.32 Gbp 2611 3.32 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 24 November 2024
aManAur1.MT.20241124.fasta.gz (6.2 KiB)

Quality: not computed
Assembly Metadata
aManAur1.yaml (view)
species: Mantella aurantiaca
specimen: aManAur1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Mantella_aurantiaca/aManAur1/assembly_vgp_HiC_2.0/aManAur1.HiC.hap1.20241124.fasta.gz 
hap2: s3://genomeark/species/Mantella_aurantiaca/aManAur1/assembly_vgp_HiC_2.0/aManAur1.HiC.hap2.20241124.fasta.gz 
pretext_hap1: s3://genomeark/species/Mantella_aurantiaca/aManAur1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aManAur1_hap1__s2_heatmap.pretext 
pretext_hap2: s3://genomeark/species/Mantella_aurantiaca/aManAur1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aManAur1_hap2__s2_heatmap.pretext  
kmer_spectra_img: s3://genomeark/species/Mantella_aurantiaca/aManAur1/assembly_vgp_HiC_2.0/evaluation/merqury/aManAur1_png/
pacbio_read_dir: s3://genomeark/species/Mantella_aurantiaca/aManAur1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Mantella_aurantiaca/aManAur1/genomic_data/arima/
mito: s3://genomeark/species/Mantella_aurantiaca/aManAur1/assembly_MT_rockefeller/aManAur1.MT.20241124.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of aManAur1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS. The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. This is a VGP Phase 1 species we are submitting for dual curation.
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.