Characidium zebra

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fChaZeb1 45.20 Gbp N/A 19.3 GiB
fChaZeb2 66.22 Gbp N/A 26.8 GiB
PacBio HiFi (.bam) fChaZeb1 47.08 Gbp N/A 144.2 GiB
fChaZeb2 67.82 Gbp N/A 213.4 GiB
Arima fChaZeb2 103.18 Gbp N/A 55.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 3 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fChaZeb1 PacBio HiFi (.fq) 45.20 Gbp N/A 19.3 GiB
PacBio HiFi (.bam) 47.08 Gbp N/A 144.2 GiB
fChaZeb2 PacBio HiFi (.fq) 66.22 Gbp N/A 26.8 GiB
PacBio HiFi (.bam) 67.82 Gbp N/A 213.4 GiB
Arima 103.18 Gbp N/A 55.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 3 June 2025.
Assemblies
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 4 April 2025
fChaZeb1.MT.20250404.fasta.gz (17.0 KiB)

Quality: not computed
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 28 October 2025
fChaZeb2.HiC.hap1.20251028.fasta.gz (286.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 24.74 Mbp 2 74.61 Mbp
20 10 21.07 Mbp 4 50.82 Mbp
30 17 17.80 Mbp 6 50.10 Mbp
40 24 14.33 Mbp 9 47.80 Mbp
50 33 12.66 Mbp 12 43.68 Mbp
60 44 10.68 Mbp 14 42.65 Mbp
70 58 6.72 Mbp 17 40.98 Mbp
80 85 3.47 Mbp 20 38.44 Mbp
90 146 1.35 Mbp 24 35.19 Mbp
100 626 14.56 Kbp 315 14.56 Kbp
1.000x 626 1.22 Gbp 315 1.22 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 28 October 2025
fChaZeb2.HiC.hap2.20251028.fasta.gz (284.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 23.93 Mbp 2 75.90 Mbp
20 10 21.22 Mbp 4 55.02 Mbp
30 16 17.23 Mbp 6 50.88 Mbp
40 23 14.04 Mbp 8 50.03 Mbp
50 33 11.93 Mbp 11 46.42 Mbp
60 44 9.73 Mbp 14 42.37 Mbp
70 59 6.68 Mbp 16 41.68 Mbp
80 84 3.25 Mbp 19 39.60 Mbp
90 142 1.43 Mbp 23 35.66 Mbp
100 513 12.57 Kbp 196 12.57 Kbp
1.000x 513 1.21 Gbp 196 1.21 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 28 October 2025
fChaZeb2.MT.20251028.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fChaZeb2.yml (view)
species: Characidium zebra
specimem: fChaZeb2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Characidium_zebra/fChaZeb2/assembly_vgp_HiC_2.0/fChaZeb2.HiC.hap1.20251028.fasta.gz
hap2: s3://genomeark/species/Characidium_zebra/fChaZeb2/assembly_vgp_HiC_2.0/fChaZeb2.HiC.hap2.20251028.fasta.gz
pretext_hap1: s3://genomeark/species/Characidium_zebra/fChaZeb2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fChaZeb2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Characidium_zebra/fChaZeb2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fChaZeb2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Characidium_zebra/fChaZeb2/assembly_vgp_HiC_2.0/evaluation/merqury/fChaZeb2_png/
pacbio_read_dir: s3://genomeark/species/Characidium_zebra/fChaZeb2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Characidium_zebra/fChaZeb2/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.5)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.1) with mapq=10
  - VGP9 decontamination workflow (v1.1) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fChaZeb2 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 merqury k-mer plots suggests that there might be some haplotigs. Manual examination show that the k-mers that have 2 copies in the assembly at the coverage range for diploid peak are scattered across scaffolds with no obvious indication of haplotigs. Hence, no track is injected in the pre-curation pretextmap. 
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.