Anadara tuberculosa

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


CC0 1.0 Hans Muller (Naturalis Biodiversity Center/Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 29 May 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 29 May 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 10 July 2023
xbAnaTube1.HiC.hap1.20230710.fasta.gz (225.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 61 1.08 Mbp 1 96.37 Mbp
20 153 0.81 Mbp 3 51.10 Mbp
30 272 0.65 Mbp 5 44.95 Mbp
40 420 0.52 Mbp 6 44.48 Mbp
50 603 426.88 Kbp 8 41.31 Mbp
60 829 336.37 Kbp 11 36.92 Mbp
70 1115 266.88 Kbp 13 33.46 Mbp
80 1487 197.06 Kbp 16 29.22 Mbp
90 2053 114.31 Kbp 21 5.06 Mbp
100 3654 6.00 Kbp 1059 6.00 Kbp
1.000x 3654 0.86 Gbp 1059 0.86 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 10 July 2023
xbAnaTube1.HiC.hap2.20230710.fasta.gz (233.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 10 7.87 Mbp 2 56.98 Mbp
20 23 5.91 Mbp 3 56.77 Mbp
30 40 4.95 Mbp 5 52.03 Mbp
40 59 4.28 Mbp 7 48.90 Mbp
50 82 3.60 Mbp 9 44.78 Mbp
60 109 2.93 Mbp 10 44.69 Mbp
70 144 2.24 Mbp 12 43.83 Mbp
80 187 1.80 Mbp 15 38.20 Mbp
90 249 1.07 Mbp 17 34.32 Mbp
100 567 12.39 Kbp 178 12.39 Kbp
1.000x 567 0.88 Gbp 178 0.89 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/xbAnaTube1.yml (view)
species: Anadara tuberculosa
specimen: xbAnaTube1
projects: 
  - vgp
hap1: s3://genomeark/species/Anadara_tuberculosa/xbAnaTube1/assembly_vgp_HiC_2.0/xbAnaTube1.HiC.hap1.20230710.fasta.gz
hap2: s3://genomeark/species/Anadara_tuberculosa/xbAnaTube1/assembly_vgp_HiC_2.0/xbAnaTube1.HiC.hap2.20230710.fasta.gz
pretext_hap1: s3://genomeark/species/Anadara_tuberculosa/xbAnaTube1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/xbAnaTube1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Anadara_tuberculosa/xbAnaTube1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/xbAnaTube1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Anadara_tuberculosa/xbAnaTube1/assembly_vgp_HiC_2.0/evaluation/merqury/xbAnaTube1_png/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of xbAnaTube1, resulting in two complete haplotypes. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit.
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.