Mixophyes fleayi

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) aMixFle1 282.66 Gbp N/A 654.0 GiB
PacBio HiFi (.fq) aMixFle1 73.41 Gbp N/A 55.5 GiB
PacBio HiFi (.bam) aMixFle1 73.32 Gbp N/A 252.6 GiB
Arima aMixFle1 174.42 Gbp N/A 90.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 25 September 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aMixFle1 PacBio HiFi (subreads) 282.66 Gbp N/A 654.0 GiB
PacBio HiFi (.fq) 73.41 Gbp N/A 55.5 GiB
PacBio HiFi (.bam) 73.32 Gbp N/A 252.6 GiB
Arima 174.42 Gbp N/A 90.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 25 September 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 29 March 2024
aMixFle1.hap1.cur.20240329.fa.gz (811.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 21 11.90 Mbp 1 463.65 Mbp
20 49 9.09 Mbp 2 377.54 Mbp
30 88 6.58 Mbp 3 349.19 Mbp
40 138 5.20 Mbp 3 349.19 Mbp
50 203 4.05 Mbp 4 346.62 Mbp
60 289 3.00 Mbp 5 279.95 Mbp
70 406 2.13 Mbp 7 154.98 Mbp
80 580 1.30 Mbp 9 133.96 Mbp
90 914 0.55 Mbp 11 100.07 Mbp
100 4227 1 bp 2806 10.33 Kbp
1.000x 4227 2.97 Gbp 2806 2.97 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 2 February 2024
aMixFle1.hap2.cur.20240202.fa.gz (732.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 18 12.74 Mbp 1 470.31 Mbp
20 44 9.77 Mbp 2 381.77 Mbp
30 77 7.48 Mbp 3 347.89 Mbp
40 122 5.75 Mbp 3 347.89 Mbp
50 178 4.48 Mbp 4 343.39 Mbp
60 251 3.51 Mbp 5 279.22 Mbp
70 347 2.61 Mbp 6 228.91 Mbp
80 483 1.66 Mbp 8 143.42 Mbp
90 729 0.85 Mbp 10 106.04 Mbp
100 2297 1.66 Kbp 914 9.99 Kbp
1.000x 2297 2.87 Gbp 914 2.88 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.