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_vgp_HiC_2.0 from 24 November 2024
aManAur1.HiC.hap1.20241124.fasta.gz (821.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 0 0
20 0 0
30 0 0
40 0 0
50 0 0
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.000x 0 0
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 24 November 2024
aManAur1.HiC.hap2.20241124.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 34 7.24 Mbp 1 0.89 Gbp
20 87 5.35 Mbp 1 0.89 Gbp
30 159 4.02 Mbp 2 469.89 Mbp
40 254 3.06 Mbp 2 469.89 Mbp
50 380 2.26 Mbp 3 327.89 Mbp
60 552 1.62 Mbp 5 183.02 Mbp
70 803 1.08 Mbp 7 162.53 Mbp
80 1214 0.59 Mbp 9 134.86 Mbp
90 2057 254.04 Kbp 12 101.84 Mbp
100 6524 3.41 Kbp 2654 3.41 Kbp
1.000x 6524 3.31 Gbp 2654 3.31 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.