Atractosteus spatula

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fAtrSpa1 81.08 Gbp N/A 43.8 GiB
PacBio HiFi (.bam) fAtrSpa1 81.42 Gbp N/A 331.1 GiB
Arima fAtrSpa1 54.67 Gbp N/A 29.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 April 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fAtrSpa1 PacBio HiFi (.fq) 81.08 Gbp N/A 43.8 GiB
PacBio HiFi (.bam) 81.42 Gbp N/A 331.1 GiB
Arima 54.67 Gbp N/A 29.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 April 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 21 April 2024
fAtrSpa1.HiC.hap1.20240421.fasta.gz (306.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 48.75 Mbp 2 76.71 Mbp
20 5 39.48 Mbp 3 74.80 Mbp
30 8 33.86 Mbp 5 65.43 Mbp
40 12 28.57 Mbp 7 62.18 Mbp
50 16 24.56 Mbp 9 55.31 Mbp
60 21 21.07 Mbp 11 46.49 Mbp
70 27 16.46 Mbp 13 38.75 Mbp
80 37 9.55 Mbp 19 17.00 Mbp
90 57 2.30 Mbp 28 7.14 Mbp
100 411 11.39 Kbp 346 11.39 Kbp
1.000x 411 1.12 Gbp 346 1.12 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 21 April 2024
fAtrSpa1.HiC.hap2.20240421.fasta.gz (317.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 49.53 Mbp 2 79.37 Mbp
20 6 38.25 Mbp 4 74.65 Mbp
30 9 31.57 Mbp 5 65.16 Mbp
40 13 27.17 Mbp 7 65.09 Mbp
50 18 23.01 Mbp 9 54.68 Mbp
60 24 18.13 Mbp 12 44.25 Mbp
70 30 17.08 Mbp 16 19.29 Mbp
80 40 9.58 Mbp 22 17.71 Mbp
90 60 2.89 Mbp 33 6.79 Mbp
100 323 18.98 Kbp 281 18.98 Kbp
1.000x 323 1.20 Gbp 281 1.20 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 21 April 2024
fAtrSpa1.MT.20240421.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fAtrSpa1.yml (view)
species: Atractosteus spatula
specimen: fAtrSpa1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Atractosteus_spatula/fAtrSpa1/assembly_vgp_HiC_2.0/fAtrSpa1.HiC.hap1.20240421.fasta.gz
hap2: s3://genomeark/species/Atractosteus_spatula/fAtrSpa1/assembly_vgp_HiC_2.0/fAtrSpa1.HiC.hap2.20240421.fasta.gz
pretext_hap1: s3://genomeark/species/Atractosteus_spatula/fAtrSpa1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fAtrSpa1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Atractosteus_spatula/fAtrSpa1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fAtrSpa1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Atractosteus_spatula/fAtrSpa1/assembly_vgp_HiC_2.0/evaluation/merqury/fAtrSpa1_png/
pacbio_read_dir: s3://genomeark/species/Atractosteus_spatula/fAtrSpa1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Atractosteus_spatula/fAtrSpa1/genomic_data/arima/
mito: s3://genomeark/species/Atractosteus_spatula/fAtrSpa1/assembly_MT_rockefeller/fAtrSpa1.MT.20240421.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fAtrSpa1, 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. 
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.