Mixophyes fleayi

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aMixFle1 73.41 Gbp N/A 55.5 GiB
Arima aMixFle1 174.42 Gbp N/A 90.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 July 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aMixFle1 PacBio HiFi (.fq) 73.41 Gbp N/A 55.5 GiB
Arima 174.42 Gbp N/A 90.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 July 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 29 August 2023
aMixFle1.hap1.decontam.20230829.fasta.gz (738.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 21 11.90 Mbp 1 462.96 Mbp
20 50 9.09 Mbp 2 377.10 Mbp
30 87 6.69 Mbp 3 346.62 Mbp
40 137 5.22 Mbp 4 346.52 Mbp
50 202 4.05 Mbp 4 346.52 Mbp
60 288 3.00 Mbp 5 279.95 Mbp
70 405 2.13 Mbp 7 154.98 Mbp
80 581 1.29 Mbp 9 133.06 Mbp
90 915 0.55 Mbp 12 83.49 Mbp
100 4223 10.33 Kbp 2822 10.33 Kbp
1.000x 4223 2.97 Gbp 2822 2.98 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 29 August 2023
aMixFle1.hap2.decontam.20230829.fasta.gz (732.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 18 12.74 Mbp 1 463.83 Mbp
20 44 9.77 Mbp 2 380.43 Mbp
30 77 7.48 Mbp 3 342.93 Mbp
40 122 5.75 Mbp 3 342.93 Mbp
50 178 4.48 Mbp 4 332.08 Mbp
60 250 3.52 Mbp 5 279.22 Mbp
70 346 2.62 Mbp 6 228.91 Mbp
80 481 1.67 Mbp 8 143.42 Mbp
90 725 0.85 Mbp 11 99.51 Mbp
100 2284 9.99 Kbp 929 9.99 Kbp
1.000x 2284 2.87 Gbp 929 2.87 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/aMixFle1_hap1.yml (view)
species: Mixophyes fleayi 
specimen: aMixFle1 
projects:  
  - vgp 
data_location: S3 
release_to: S3 
haplotype_to_curate: hap1 
hap1: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/assembly_vgp_HiC_2.0/aMixFle1.HiC.hap1.20230828.fasta.gz 
hap2: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/assembly_vgp_HiC_2.0/aMixFle1.HiC.hap2.20230828.fasta.gz 
pretext_hap1: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aMixFle1_hap1_s2.pretext 
pretext_hap2: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aMixFle1_hap2_s2.pretext 
kmer_spectra_img: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/assembly_vgp_HiC_2.0/evaluation/merqury/aMixFle1_png/ 
pacbio_read_dir: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/genomic_data/pacbio_hifi/ 
pacbio_read_type: hifi 
bionano_cmap_dir: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/genomic_data/bionano/ 
hic_read_dir: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/genomic_data/arima/ 
pipeline: 
  - hifiasm (0.19.3+galaxy0) 
  - solve (3.7) 
  - yahs (1.2a.2+galaxy1) 
assembled_by_group: Rockefeller 
notes: This was a hifiasm-HiC assembly of aMixFle1, resulting in two complete haplotypes. Kmer spectra indicate a homogametic specimen. This individual had bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. MitoHiFi failed on the reads. 
assembly_vgp_HiC_2.0/aMixFle1_hap2.yml (view)
species: Mixophyes fleayi 
specimen: aMixFle1 
projects:  
  - vgp 
data_location: S3 
release_to: S3 
haplotype_to_curate: hap2 
hap1: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/assembly_vgp_HiC_2.0/aMixFle1.HiC.hap1.20230828.fasta.gz 
hap2: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/assembly_vgp_HiC_2.0/aMixFle1.HiC.hap2.20230828.fasta.gz 
pretext_hap1: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aMixFle1_hap1_s2.pretext 
pretext_hap2: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aMixFle1_hap2_s2.pretext 
kmer_spectra_img: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/assembly_vgp_HiC_2.0/evaluation/merqury/aMixFle1_png/ 
pacbio_read_dir: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/genomic_data/pacbio_hifi/ 
pacbio_read_type: hifi 
bionano_cmap_dir: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/genomic_data/bionano/ 
hic_read_dir: s3://genomeark/species/Mixophyes_fleayi/aMixFle1/genomic_data/arima/ 
pipeline: 
  - hifiasm (0.19.3+galaxy0) 
  - solve (3.7) 
  - yahs (1.2a.2+galaxy1) 
assembled_by_group: Rockefeller 
notes: This was a hifiasm-HiC assembly of aMixFle1, resulting in two complete haplotypes. Kmer spectra indicate a homogametic specimen. This individual had bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. MitoHiFi failed on the reads. 
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.