Crotalus willardi

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rCroWil1 107.72 Gbp N/A 52.4 GiB
PacBio HiFi (.bam) rCroWil1 110.39 Gbp N/A 367.0 GiB
Arima rCroWil1 160.25 Gbp N/A 84.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 March 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rCroWil1 PacBio HiFi (.fq) 107.72 Gbp N/A 52.4 GiB
PacBio HiFi (.bam) 110.39 Gbp N/A 367.0 GiB
Arima 160.25 Gbp N/A 84.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 March 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 19 May 2026
rCroWil1.HiC.hap1.20260519.fasta.gz (419.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 111.78 Mbp 1 362.00 Mbp
20 3 103.92 Mbp 1 362.00 Mbp
30 5 77.08 Mbp 2 302.88 Mbp
40 7 64.36 Mbp 2 302.88 Mbp
50 10 57.06 Mbp 3 285.05 Mbp
60 13 40.42 Mbp 4 186.22 Mbp
70 19 23.04 Mbp 5 126.56 Mbp
80 31 7.07 Mbp 6 103.81 Mbp
90 72 2.49 Mbp 8 43.68 Mbp
100 315 16.49 Kbp 26 16.49 Kbp
1.000x 315 1.63 Gbp 26 1.63 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 19 May 2026
rCroWil1.HiC.hap2.20260519.fasta.gz (376.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 99.91 Mbp 1 359.62 Mbp
20 3 99.70 Mbp 1 359.62 Mbp
30 5 78.96 Mbp 2 281.91 Mbp
40 7 70.04 Mbp 2 281.91 Mbp
50 9 62.01 Mbp 3 205.19 Mbp
60 11 57.23 Mbp 4 125.74 Mbp
70 17 18.96 Mbp 5 103.97 Mbp
80 31 5.79 Mbp 6 95.39 Mbp
90 73 1.88 Mbp 10 22.98 Mbp
100 387 20.07 Kbp 68 23.82 Kbp
1.000x 387 1.46 Gbp 68 1.46 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 11 May 2026
rCroWil1.MT.20260511.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rCroWil1.yml (view)
species: Crotalus willardi
specimen: rCroNil1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Crotalus_willardi/rCroNil1/assembly_vgp_HiC_2.0/rCroWil1.HiC.hap1.20260519.fasta.gz
hap2: s3://genomeark/species/Crotalus_willardi/rCroNil1/assembly_vgp_HiC_2.0/rCroWil1.HiC.hap2.20260519.fasta.gz
pretext_hap1: s3://genomeark/species/Crotalus_willardi/rCroWil1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/rCroWil1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Crotalus_willardi/rCroNil1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/rCroWil1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Crotalus_willardi/rCroNil1/assembly_vgp_HiC_2.0/evaluation/merqury/rCroNil1_png/
pacbio_read_dir: s3://genomeark/species/Crotalus_willardi/rCroNil1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Crotalus_willardi/rCroNil1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.9)
  - VGP4 HiFi HiC assembly workflow (v0.6)
  - VGP4 purge_dups workflow (v0.10.5)
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10
  - VGP9 decontamination workflow (v0.1.3)
  - Pre-curation workflow (v2.4) with mapq=10, keep HiC duplicates and generate high-resolution map
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.