Chitra chitra

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rChiChi1 159.86 Gbp 72.95x 72.1 GiB
PacBio HiFi (.bam) rChiChi1 161.84 Gbp 73.86x 535.8 GiB
Arima rChiChi1 251.16 Gbp 114.62x 135.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.19 Gbp.
Last upload on 24 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rChiChi1 PacBio HiFi (.fq) 159.86 Gbp 72.95x 72.1 GiB
PacBio HiFi (.bam) 161.84 Gbp 73.86x 535.8 GiB
Arima 251.16 Gbp 114.62x 135.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.19 Gbp.
Last upload on 24 June 2025.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 21 August 2025
rChiChi1.pri.cur.20250821.fasta.gz (642.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 340.80 Mbp 1 346.86 Mbp
20 2 200.10 Mbp 2 264.12 Mbp
30 3 136.59 Mbp 3 200.10 Mbp
40 5 127.53 Mbp 4 137.16 Mbp
50 7 78.63 Mbp 6 131.48 Mbp
60 10 68.37 Mbp 8 75.40 Mbp
70 14 43.82 Mbp 11 54.04 Mbp
80 19 38.10 Mbp 16 42.01 Mbp
90 27 20.49 Mbp 22 27.80 Mbp
100 61 2.89 Kbp 36 26.26 Kbp
1.000x 61 2.19 Gbp 36 2.19 Gbp
NG based on genome size 2.19 Gbp.
Individual 1 Alternate Assembly
No assembly available.


Contigs Scaffolds
NG LG Len LG Len
10 - - - -
20 - - - -
30 - - - -
40 - - - -
50 - - - -
60 - - - -
70 - - - -
80 - - - -
90 - - - -
100 - - - -
0.000x - 0.0 Mbp - 0.0 Mbp
Individual 1 Haplotype 1 Assembly
No assembly available.


Contigs Scaffolds
NG LG Len LG Len
10 - - - -
20 - - - -
30 - - - -
40 - - - -
50 - - - -
60 - - - -
70 - - - -
80 - - - -
90 - - - -
100 - - - -
0.000x - 0.0 Mbp - 0.0 Mbp
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 August 2025
rChiChi1.HiC.hap2.20250806.fasta.gz (596.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 340.80 Mbp 1 346.13 Mbp
20 2 200.10 Mbp 2 264.12 Mbp
30 3 136.59 Mbp 3 200.10 Mbp
40 5 131.61 Mbp 4 137.16 Mbp
50 7 119.69 Mbp 6 131.61 Mbp
60 9 75.40 Mbp 8 75.61 Mbp
70 13 43.82 Mbp 11 57.60 Mbp
80 18 38.10 Mbp 15 47.52 Mbp
90 26 20.49 Mbp 21 30.82 Mbp
100 55 20.23 Kbp 36 26.26 Kbp
1.000x 55 2.19 Gbp 36 2.19 Gbp
NG based on genome size 2.19 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/rChiChi1.yml (view)
species: Chitra chitra
specimem: rChiChi1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: false
hap2: s3://genomeark/species/Chitra_chitra/rChiChi1/assembly_vgp_HiC_2.0/rChiChi1.HiC.hap2.20250806.fasta.gz
pretext_hap2: s3://genomeark/species/Chitra_chitra/rChiChi1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/rChiChi1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Chitra_chitra/rChiChi1/assembly_vgp_HiC_2.0/evaluation/merqury/rChiChi1_png/
pacbio_read_dir: s3://genomeark/species/Chitra_chitra/rChiChi1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Chitra_chitra/rChiChi1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.1)
  - VGP1 genomic profiling workflow (v0.3)
  - VGP4 HiFi HiC assembly workflow (v0.3.8)
  - VGP6 purge duplicate contigs workflow (v0.10.2)
  - VGP8 HiC scaffolding workflow (v2.0) 
  - VGP9 decontamination workflow (v0.7) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6) on only one haplotype
notes: 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. HiFiasm produced two haplotype assemblies, one highly complete while the other largely missing. It is probable that the individual is highly inbred, resulting in a depletion of heterozygosity across the genome and thus no signals for phasing in HiFiasm. Run VGP6 purge_dups workflow to remove the haplotigs in Hap2. Scaffolding was run on the hap2 only as well. 
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.