Lampris incognitus

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Resource Primary Assembly Alternate Assembly
GenBank fLamInc1: GCA_029633845.1 fLamInc1: GCA_029633865.1
ENA fLamInc1: GCA_029633845.1 fLamInc1: GCA_029633865.1
UCSC Genome Browser fLamInc1: GCA_029633845.1 fLamInc1: GCA_029633865.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fLamInc1 46.34 Gbp N/A 35.5 GiB
Arima fLamInc1 101.01 Gbp N/A 49.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 October 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fLamInc1 PacBio HiFi (.fq) 46.34 Gbp N/A 35.5 GiB
Arima 101.01 Gbp N/A 49.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 6 October 2022.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 25 March 2023
fLamInc1.hap1.decon.20230325.fasta.gz (391.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 25 4.25 Mbp 1 137.31 Mbp
20 74 2.29 Mbp 2 112.01 Mbp
30 152 1.60 Mbp 3 77.21 Mbp
40 261 1.17 Mbp 5 68.27 Mbp
50 409 0.86 Mbp 8 62.04 Mbp
60 604 0.65 Mbp 10 58.11 Mbp
70 868 483.98 Kbp 13 46.14 Mbp
80 1236 324.08 Kbp 16 42.80 Mbp
90 1860 169.05 Kbp 20 26.98 Mbp
100 4178 1.21 Kbp 1058 10.54 Kbp
1.000x 4179 1.48 Gbp 1059 1.48 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 25 March 2023
fLamInc1.hap2.cur.20230325.fasta.gz (388.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 22 4.47 Mbp 0 155.00 Mbp
20 66 2.66 Mbp 1 152.47 Mbp
30 136 1.70 Mbp 3 75.57 Mbp
40 238 1.22 Mbp 5 69.76 Mbp
50 377 0.91 Mbp 7 62.61 Mbp
60 564 0.68 Mbp 9 60.22 Mbp
70 819 491.58 Kbp 12 54.96 Mbp
80 1177 335.25 Kbp 15 48.45 Mbp
90 1768 180.54 Kbp 18 40.30 Mbp
100 3650 1.03 Kbp 537 12.34 Kbp
1.000x 3651 1.47 Gbp 538 1.47 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/fLamInc1_hap2.yml (view)
species: Lampris incognitus
specimen: fLamInc1
projects: 
  - vgp
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Lampris_incognitus/fLamInc1/assembly_vgp_HiC_2.0/fLamInc1.HiC.hap1.20230206.fasta.gz
hap2: s3://genomeark/species/Lampris_incognitus/fLamInc1/assembly_vgp_HiC_2.0/fLamInc1.HiC.hap2.20230206.fasta.gz
pretext_hap1: s3://genomeark/species/Lampris_incognitus/fLamInc1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fLamInc1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Lampris_incognitus/fLamInc1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fLamInc1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Lampris_incognitus/fLamInc1/assembly_vgp_HiC_2.0/evaluation/merqury/fLamInc1_png/
pacbio_read_dir: s3://genomeark/species/Lampris_incognitus/fLamInc1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Lampris_incognitus/fLamInc1/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1+galaxy4)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of fLamInc1, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The kmer spectra indicates a homogametic specimen. We are submitting haplotype 2 for 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.