Dibamus smithi

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rDibSmi1 76.46 Gbp N/A 35.8 GiB
PacBio HiFi (.bam) rDibSmi1 78.81 Gbp N/A 260.7 GiB
Arima rDibSmi1 162.48 Gbp N/A 89.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 September 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rDibSmi1 PacBio HiFi (.fq) 76.46 Gbp N/A 35.8 GiB
PacBio HiFi (.bam) 78.81 Gbp N/A 260.7 GiB
Arima 162.48 Gbp N/A 89.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 September 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 3 December 2024
rDibSmi1.hap1.cur.20241203.fasta.gz (662.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 48.44 Mbp 1 301.69 Mbp
20 10 39.78 Mbp 2 250.08 Mbp
30 16 33.25 Mbp 3 189.33 Mbp
40 23 25.51 Mbp 5 170.22 Mbp
50 34 18.16 Mbp 6 146.22 Mbp
60 48 14.58 Mbp 8 131.56 Mbp
70 66 10.58 Mbp 9 128.83 Mbp
80 92 6.82 Mbp 11 93.78 Mbp
90 137 3.43 Mbp 15 50.12 Mbp
100 600 9.69 Kbp 326 9.69 Kbp
1.000x 600 2.28 Gbp 326 2.28 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 3 December 2024
rDibSmi1.hap2.cur.20241203.fasta.gz (527.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 49.48 Mbp 1 250.59 Mbp
20 8 43.01 Mbp 2 189.17 Mbp
30 12 38.71 Mbp 3 170.44 Mbp
40 17 31.68 Mbp 4 146.48 Mbp
50 24 26.44 Mbp 6 131.87 Mbp
60 32 18.64 Mbp 7 129.18 Mbp
70 44 11.19 Mbp 9 93.81 Mbp
80 62 8.60 Mbp 11 66.28 Mbp
90 93 3.89 Mbp 14 49.05 Mbp
100 917 6.86 Kbp 720 6.86 Kbp
1.000x 917 1.82 Gbp 720 1.82 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 28 September 2024
rDibSmi1.MT.20240928.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/rDibSmi1.yml (view)
species: Dibamus smithi
specimen: mDibSmi1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Dibamus_Smithi/rDibSmi1/assembly_vgp_HiC_2.0/evaluation/rDibSmi1.HiC.hap2.20240928.fasta.gz
hap2: s3://genomeark/species/Dibamus_Smithi/rDibSmi1/assembly_vgp_HiC_2.0/evaluation/rDibSmi1.HiC.hap1.20240928.fasta.gz
pretext_hap1: s3://genomeark/species/Dibamus_Smithi/rDibSmi1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rDibSmi1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Dibamus_Smithi/rDibSmi1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rDibSmi1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Dibamus_Smithi/rDibSmi1/species/Dibamus_Smithi/mDibSmi1/assembly_vgp_HiC_2.0/evaluation/merqury/mDibSmi1_png
pacbio_read_dir: s3://genomeark/species/Dibamus_Smithi/rDibSmi1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Dibamus_Smithi/rDibSmi1/genomic_data/arima/
mito: s3://genomeark/species/species/Dibamus_Smithi/rDibSmi1/assembly_MT_rockefeller/rDibSmi1.MT.20240928.fasta
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of rDibSmi1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS. The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. This is a VGP Phase 1 species we are submitting for dual curation.
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.