Spea multiplicata

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aSpeMul1 57.65 Gbp N/A 28.9 GiB
PacBio HiFi (.bam) aSpeMul1 57.15 Gbp N/A 230.9 GiB
Arima aSpeMul1 120.53 Gbp N/A 62.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aSpeMul1 PacBio HiFi (.fq) 57.65 Gbp N/A 28.9 GiB
PacBio HiFi (.bam) 57.15 Gbp N/A 230.9 GiB
Arima 120.53 Gbp N/A 62.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 28 March 2024
aSpeMul1.HiC.hap1.20240328.fasta.gz (259.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 51.72 Mbp 1 157.61 Mbp
20 4 45.96 Mbp 2 127.71 Mbp
30 6 37.68 Mbp 2 127.71 Mbp
40 10 21.14 Mbp 3 109.24 Mbp
50 15 17.21 Mbp 4 107.89 Mbp
60 22 11.42 Mbp 5 99.64 Mbp
70 32 6.94 Mbp 6 83.22 Mbp
80 53 3.05 Mbp 8 44.86 Mbp
90 108 1.05 Mbp 10 38.61 Mbp
100 759 11.43 Kbp 586 11.43 Kbp
1.000x 759 0.95 Gbp 586 0.95 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 28 March 2024
aSpeMul1.HiC.hap2.20240328.fasta.gz (260.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 50.32 Mbp 1 159.13 Mbp
20 4 43.22 Mbp 2 127.22 Mbp
30 7 29.99 Mbp 2 127.22 Mbp
40 11 22.47 Mbp 3 109.03 Mbp
50 17 12.31 Mbp 4 103.61 Mbp
60 26 8.23 Mbp 5 101.77 Mbp
70 40 5.70 Mbp 7 45.13 Mbp
80 61 3.29 Mbp 9 38.86 Mbp
90 110 1.11 Mbp 12 28.99 Mbp
100 540 14.06 Kbp 357 14.06 Kbp
1.000x 540 0.95 Gbp 357 0.95 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 28 March 2024
aSpeMul1.MT.20240328.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/aSpeMul1.yml (view)
species: Spea multiplicata
specimen: aSpeMul1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Spea_multiplicata/aSpeMul1/assembly_vgp_HiC_2.0/aSpeMul1.HiC.hap1.20240328.fasta.gz
hap2: s3://genomeark/species/Spea_multiplicata/aSpeMul1/assembly_vgp_HiC_2.0/aSpeMul1.HiC.hap2.20240328.fasta.gz
pretext_hap1: s3://genomeark/species/Spea_multiplicata/aSpeMul1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aSpeMul1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Spea_multiplicata/aSpeMul1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aSpeMul1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Spea_multiplicata/aSpeMul1/assembly_vgp_HiC_2.0/evaluation/merqury/aSpeMul1_png/
mito: s3://genomeark/species/Spea_multiplicata/aSpeMul1/assembly_MT_rockefeller/aSpeMul1.MT.20240328.fasta.gz
pacbio_read_dir: s3://genomeark/species/Spea_multiplicata/aSpeMul1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Spea_multiplicata/aSpeMul1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of aSpeMul1, resulting in two complete haplotypes. The HiC prep kit used was Arima, so the HiC reads require trimming 5 bp off the 5' end. The assembly was performed on the Rockefeller University VGL instance. 
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.