Bothrops pictus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rBotPic1 171.61 Gbp N/A 82.5 GiB
PacBio HiFi (.bam) rBotPic1 175.10 Gbp N/A 577.2 GiB
Arima rBotPic1 1317.06 Gbp N/A 645.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 3 June 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rBotPic1 PacBio HiFi (.fq) 171.61 Gbp N/A 82.5 GiB
PacBio HiFi (.bam) 175.10 Gbp N/A 577.2 GiB
Arima 1317.06 Gbp N/A 645.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 3 June 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 1 June 2026
rBotPic1.hap1.cur.20260601.fasta.gz (494.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 105.56 Mbp 1 374.17 Mbp
20 4 78.05 Mbp 1 374.17 Mbp
30 6 73.10 Mbp 2 288.48 Mbp
40 9 61.60 Mbp 3 225.40 Mbp
50 13 40.97 Mbp 4 145.52 Mbp
60 18 27.67 Mbp 5 131.10 Mbp
70 26 16.92 Mbp 6 120.87 Mbp
80 45 5.82 Mbp 8 98.67 Mbp
90 103 1.85 Mbp 11 27.04 Mbp
100 597 3.43 Kbp 204 16.13 Kbp
1.000x 597 1.79 Gbp 204 1.79 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 1 June 2026
rBotPic1.hap2.cur.20260601.fasta.gz (387.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 89.41 Mbp 1 368.31 Mbp
20 4 72.64 Mbp 1 368.31 Mbp
30 6 70.86 Mbp 2 286.02 Mbp
40 8 69.20 Mbp 2 286.02 Mbp
50 11 44.24 Mbp 3 217.05 Mbp
60 14 33.74 Mbp 4 130.04 Mbp
70 20 21.93 Mbp 5 104.97 Mbp
80 30 10.53 Mbp 6 98.42 Mbp
90 62 2.35 Mbp 9 27.61 Mbp
100 407 15.50 Kbp 125 22.05 Kbp
1.000x 407 1.48 Gbp 125 1.48 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 29 January 2026
rBotPic1.MT.20260129.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rBotPic1.yml (view)
species: Bothrops pictus
specimem: rBotPic1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Bothrops_pictus/rBotPic1/assembly_vgp_HiC_2.0/rBotPic1.HiC.hap1.20251210.fasta.gz
hap2: s3://genomeark/species/Bothrops_pictus/rBotPic1/assembly_vgp_HiC_2.0/rBotPic1.HiC.hap2.20251210.fasta.gz
pretext_hap1: s3://genomeark/species/Bothrops_pictus/rBotPic1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/rBotPic1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Bothrops_pictus/rBotPic1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/rBotPic1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Bothrops_pictus/rBotPic1/assembly_vgp_HiC_2.0/evaluation/merqury/rBotPic1_png/
pacbio_read_dir: s3://genomeark/species/Bothrops_pictus/rBotPic1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Bothrops_pictus/rBotPic1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.6)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.2) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of rBotPic1 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 plots show some haplotigs in hap1 and missing k-mers in hap2 in the heterozygote peak. Running VGP6 purge-dups workflow (v0.10.4) did not appear to remove haplotigs. Hence, I output the original assemblies without purging. For mitogenome assembly, the first mitoHiFi attempt using all HiFi reads resulted in a ~40kbp mitogenome, which contained some NUMT sequences. To filter out NUMT reads, I mapped HiFi reads onto NC_039649.1 and remove reads with >400bp soft-clipping. The mitoHiFi annotated 33 genes, while MITOS2 annotated 36 genes (missing nad4l). The NCBI blast showed the mitogenome belongs to the same genus Bothrops. 
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.