Crocodylus niloticus

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rCroNil1 188.37 Gbp N/A 87.5 GiB
PacBio HiFi (.bam) rCroNil1 191.56 Gbp N/A 622.9 GiB
Arima rCroNil1 189.91 Gbp N/A 106.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rCroNil1 PacBio HiFi (.fq) 188.37 Gbp N/A 87.5 GiB
PacBio HiFi (.bam) 191.56 Gbp N/A 622.9 GiB
Arima 189.91 Gbp N/A 106.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 2 September 2025
rCroNil1.HiC.hap1.20250902.fasta.gz (623.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 209.29 Mbp 1 486.44 Mbp
20 3 162.18 Mbp 1 486.44 Mbp
30 4 152.76 Mbp 2 316.53 Mbp
40 6 126.48 Mbp 3 259.24 Mbp
50 8 110.87 Mbp 4 220.68 Mbp
60 10 94.89 Mbp 5 177.53 Mbp
70 14 62.83 Mbp 7 126.48 Mbp
80 18 44.39 Mbp 9 93.17 Mbp
90 25 27.33 Mbp 12 77.56 Mbp
100 158 19.94 Kbp 130 19.94 Kbp
1.000x 158 2.35 Gbp 130 2.35 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 2 September 2025
rCroNil1.HiC.hap2.20250902.fasta.gz (622.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 260.61 Mbp 1 482.96 Mbp
20 2 208.40 Mbp 1 482.96 Mbp
30 4 144.78 Mbp 2 315.14 Mbp
40 6 126.79 Mbp 3 260.61 Mbp
50 8 112.06 Mbp 4 230.16 Mbp
60 10 93.87 Mbp 5 219.07 Mbp
70 13 48.55 Mbp 6 176.72 Mbp
80 18 38.94 Mbp 8 100.33 Mbp
90 26 25.40 Mbp 11 76.98 Mbp
100 112 23.10 Kbp 81 23.10 Kbp
1.000x 112 2.34 Gbp 81 2.34 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 28 August 2025
rCroNil1.MT.20250828.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rCroNil1.yml (view)
species: Crocodylus niloticus
specimem: rCroNil1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Crocodylus_niloticus/rCroNil1/assembly_vgp_HiC_2.0/rCroNil1.HiC.hap1.20250902.fasta.gz
hap2: s3://genomeark/species/Crocodylus_niloticus/rCroNil1/assembly_vgp_HiC_2.0/rCroNil1.HiC.hap2.20250902.fasta.gz
pretext_hap1: s3://genomeark/species/Crocodylus_niloticus/rCroNil1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/rCroNil1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Crocodylus_niloticus/rCroNil1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/rCroNil1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Crocodylus_niloticus/rCroNil1/assembly_vgp_HiC_2.0/evaluation/merqury/rCroNil1_png/
pacbio_read_dir: s3://genomeark/species/Crocodylus_niloticus/rCroNil1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Crocodylus_niloticus/rCroNil1/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)
  - VGP8 HiC scaffolding workflow (v2.0)
  - VGP9 decontamination workflow (v0.7) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm-HiC assembly of rCroNil1 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.
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.