Lepisosteus oculatus

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Resource Primary Assembly Alternate Assembly
GenBank fLepOcu1: GCA_040954835.1 fLepOcu1: GCA_040954845.1
ENA fLepOcu1: GCA_040954835.1 fLepOcu1: GCA_040954845.1
UCSC Genome Browser fLepOcu1: GCA_040954835.1 fLepOcu1: GCA_040954845.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fLepOcu1 60.49 Gbp N/A 31.3 GiB
PacBio HiFi (.bam) fLepOcu1 59.99 Gbp N/A 245.6 GiB
Arima fLepOcu1 75.42 Gbp N/A 39.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 February 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fLepOcu1 PacBio HiFi (.fq) 60.49 Gbp N/A 31.3 GiB
PacBio HiFi (.bam) 59.99 Gbp N/A 245.6 GiB
Arima 75.42 Gbp N/A 39.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 February 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 6 May 2024
fLepOcu1.hap1.cur.20240506.fasta.gz (273.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 45.95 Mbp 2 78.25 Mbp
20 6 34.28 Mbp 3 74.42 Mbp
30 9 26.64 Mbp 5 61.49 Mbp
40 14 21.78 Mbp 7 58.68 Mbp
50 20 16.91 Mbp 9 46.68 Mbp
60 26 15.96 Mbp 12 39.82 Mbp
70 34 14.15 Mbp 14 37.91 Mbp
80 43 10.07 Mbp 19 17.87 Mbp
90 59 3.70 Mbp 26 12.38 Mbp
100 907 9.38 Kbp 831 9.38 Kbp
1.000x 907 1.11 Gbp 831 1.11 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 6 May 2024
fLepOcu1.hap2.cur.20240506.fasta.gz (285.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 37.64 Mbp 2 78.35 Mbp
20 6 34.26 Mbp 4 66.80 Mbp
30 10 29.24 Mbp 5 61.57 Mbp
40 15 25.02 Mbp 7 60.01 Mbp
50 20 20.02 Mbp 10 47.77 Mbp
60 27 15.43 Mbp 12 42.31 Mbp
70 36 11.27 Mbp 16 23.55 Mbp
80 49 7.30 Mbp 22 16.20 Mbp
90 92 1.34 Mbp 34 2.32 Mbp
100 911 15.28 Kbp 816 15.28 Kbp
1.000x 911 1.20 Gbp 816 1.20 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 March 2024
fLepOcu1.MT.20240306.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fLepOcu1.yml (view)
species: Lepisosteus oculatus
specimen: fLepOcu1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Lepisosteus_oculatus/fLepOcu1/assembly_vgp_HiC_2.0/fLepOcu1.HiC.hap1.20240305.fasta.gz
hap2: s3://genomeark/species/Lepisosteus_oculatus/fLepOcu1/assembly_vgp_HiC_2.0/fLepOcu1.HiC.hap2.20240305.fasta.gz
pretext_hap1: s3://genomeark/species/Lepisosteus_oculatus/fLepOcu1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fLepOcu1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Lepisosteus_oculatus/fLepOcu1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fLepOcu1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Lepisosteus_oculatus/fLepOcu1/assembly_vgp_HiC_2.0/evaluation/merqury/fLepOcu1_png/
pacbio_read_dir: s3://genomeark/species/Lepisosteus_oculatus/fLepOcu1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Lepisosteus_oculatus/fLepOcu1/genomic_data/arima/
mito: s3://genomeark/species/Lepisosteus_oculatus/fLepOcu1/assembly_MT_rockefeller/fLepOcu1.MT.20240306.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fLepOcu1, 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.