Vipera latastei

snub-nosed viper

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank rVipLat1: GCA_024294585.1 rVipLat1: GCA_024294605.1
ENA rVipLat1: GCA_024294585.1 rVipLat1: GCA_024294605.1
UCSC Genome Browser rVipLat1: GCA_024294585.1 rVipLat1: GCA_024294605.1

metadata.yaml (view) (edit on github)
species:
  short_name: rVipLat
  name: Vipera latastei
  taxon_id: 246179
  common_name: snub-nosed viper
  order:
    name: Squamata
  family:
    name: Viperidae
  individuals:
    - short_name: rVipLat1
      provider: Tomàs Marqués
  genome_size: 2500000000
  genome_size_method:
  project: [ vgp ]
CC BY-NC-SA 2.0 Alexandre Roux (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) rVipLat1 1563.89 Gbp 625.56x 2.7 TiB
PacBio HiFi (.fq) rVipLat1 32.56 Gbp 13.02x 27.3 GiB
PacBio HiFi (.bam) rVipLat1 79.25 Gbp 31.70x 65.1 GiB
Bionano rVipLat1 N/A 540.22x 2.8 GiB
Arima rVipLat1 165.33 Gbp 66.13x 105.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.50 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rVipLat1 PacBio HiFi (subreads) 1563.89 Gbp 625.56x 2.7 TiB
PacBio HiFi (.fq) 32.56 Gbp 13.02x 27.3 GiB
PacBio HiFi (.bam) 79.25 Gbp 31.70x 65.1 GiB
Bionano N/A 540.22x 2.8 GiB
Arima 165.33 Gbp 66.13x 105.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.50 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 8 December 2021
rVipLat1.pri.cur.20211208.fasta.gz (466.3 MiB)

Quality: 26.7 errors/Mb (QV=45.73)

Contigs Scaffolds
NG LG Len LG Len
10 1 119.06 Mbp 0 370.63 Mbp
20 4 70.69 Mbp 1 299.85 Mbp
30 9 45.98 Mbp 2 222.49 Mbp
40 15 31.88 Mbp 3 138.01 Mbp
50 37 7.29 Mbp 5 104.94 Mbp
60 129 0.90 Mbp 10 23.63 Mbp
70 0 0
80 0 0
90 0 0
100 0 0
0.651x 825 1.63 Gbp 56 1.63 Gbp
NG based on genome size 2.50 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 8 December 2021
rVipLat1.alt.cur.20211208.fasta.gz (446.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 135 1.33 Mbp 135 1.33 Mbp
20 372 0.88 Mbp 372 0.88 Mbp
30 720 0.59 Mbp 720 0.59 Mbp
40 1249 382.16 Kbp 1249 382.16 Kbp
50 2149 196.33 Kbp 2149 196.33 Kbp
60 4892 39.74 Kbp 4892 39.74 Kbp
70 0 0
80 0 0
90 0 0
100 0 0
0.620x 6800 1.55 Gbp 6799 1.55 Gbp
NG based on genome size 2.50 Gbp.
Assembly Metadata
assembly_vgp_2.0_IBE/rVipLat1.yaml (view)
species: Vipera latastei 
specimen:  rVipLat1 
projects:  
  -VGP 
  -CBP 
primary: s3://genomeark/species/Vipera_latastei/rVipLat1/assembly_vgp_2.0_IBE/intermediates/rVipLat1_ragtag.fasta.gz 
haplotigs: s3://genomeark/species/Vipera_latastei/rVipLat1/assembly_vgp_2.0_IBE/intermediates/rVipLat1_q2.fasta.gz 
hic_bam:  s3://genomeark/species/Vipera_latastei/rVipLat1/assembly_vgp_2.0_IBE/evaluation/bam_to_create_pretext_rVipLat1.bam 
pretext: s3://genomeark/species/Vipera_latastei/rVipLat1/assembly_vgp_2.0_IBE/evaluation/assembly_FullMap.png 
kmer_spectra_img: s3://genomeark/species/Vipera_latastei/rVipLat1/assembly_vgp_2.0_IBE/evaluation/p/Merqury/pacbio/plot_pacbio_cutadapt_rVipLat1_plot.fl.png 
pipeline:  
 -hifiasm (0.13)  
 -purge_dups (1.2.5)  
 -bionano solve (3.6.1)  
 -salsa (2.2)  
 -ragtag (2.0.1) <[ flye (2.8.3) + hypo (2.4.1) + purge_dups (1.2.5) + bionano solve (3.6.1) + salsa (2.2)] 
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.