Odontesthes bonariensis

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Resource Primary Assembly Alternate Assembly
GenBank fOdoBon6: GCA_027942865.1 fOdoBon6: GCA_027942885.1
ENA fOdoBon6: GCA_027942865.1 fOdoBon6: GCA_027942885.1
UCSC Genome Browser fOdoBon6: GCA_027942865.1 fOdoBon6: GCA_027942885.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fOdoBon6 33.41 Gbp 35.32x 23.7 GiB
Arima fOdoBon6 89.99 Gbp 95.14x 46.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.95 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fOdoBon6 PacBio HiFi (.fq) 33.41 Gbp 35.32x 23.7 GiB
Arima 89.99 Gbp 95.14x 46.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.95 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 6 Primary Assembly
Version assembly_curated from 7 July 2022
fOdoBon6.pri.cur.20220707.fasta.gz (261.3 MiB)

Quality: 0.3 errors/Mb (QV=64.64)

Contigs Scaffolds
NG LG Len LG Len
10 3 23.88 Mbp 1 46.87 Mbp
20 7 19.95 Mbp 4 42.25 Mbp
30 13 16.07 Mbp 6 40.69 Mbp
40 19 12.96 Mbp 8 40.12 Mbp
50 28 9.83 Mbp 11 39.25 Mbp
60 40 6.46 Mbp 13 38.54 Mbp
70 57 4.96 Mbp 15 38.31 Mbp
80 80 3.29 Mbp 18 35.39 Mbp
90 126 1.35 Mbp 21 33.06 Mbp
100 470 10.92 Kbp 188 10.92 Kbp
1.000x 471 0.95 Gbp 189 0.95 Gbp
NG based on genome size 0.95 Gbp.
Individual 6 Alternate Assembly
Version assembly_curated from 7 July 2022
fOdoBon6.alt.cur.20220707.fasta.gz (0.1 KiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 0 0
20 0 0
30 0 0
40 0 0
50 0 0
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.000x 0 0
NG based on genome size 0.95 Gbp.
Individual 6 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 7 June 2022
fOdoBon6.HiC.hap1.20220607.fasta.gz (257.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 23.88 Mbp 2 40.16 Mbp
20 7 19.95 Mbp 4 37.98 Mbp
30 13 16.07 Mbp 7 36.05 Mbp
40 19 12.96 Mbp 9 33.35 Mbp
50 28 9.83 Mbp 12 31.77 Mbp
60 40 6.46 Mbp 15 31.39 Mbp
70 57 4.96 Mbp 18 29.87 Mbp
80 80 3.29 Mbp 22 20.46 Mbp
90 126 1.35 Mbp 37 3.80 Mbp
100 469 10.92 Kbp 319 10.92 Kbp
1.000x 470 0.95 Gbp 320 0.95 Gbp
NG based on genome size 0.95 Gbp.
Individual 6 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 7 June 2022
fOdoBon6.HiC.hap2.20220607.fasta.gz (260.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 24.55 Mbp 1 56.20 Mbp
20 7 21.25 Mbp 3 41.14 Mbp
30 12 19.23 Mbp 5 39.35 Mbp
40 18 14.04 Mbp 8 33.62 Mbp
50 27 8.49 Mbp 11 30.59 Mbp
60 40 6.51 Mbp 14 29.63 Mbp
70 57 4.97 Mbp 18 26.00 Mbp
80 84 2.83 Mbp 23 8.05 Mbp
90 135 1.14 Mbp 47 1.96 Mbp
100 468 13.80 Kbp 333 13.80 Kbp
1.000x 469 0.97 Gbp 334 0.97 Gbp
NG based on genome size 0.95 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/fOdoBon6.yaml (view)
species: Odontesthes bonariensis
specimen: fOdoBon6
projects:
  - vgp
hap1: s3://genomeark/species/Odontesthes_bonariensis/fOdoBon6/assembly_vgp_HiC_2.0/fOdoBon6.20220607.hap1.fasta.gz
hap2: s3://genomeark/species/Odontesthes_bonariensis/fOdoBon6/assembly_vgp_HiC_2.0/fOdoBon6.20220607.hap2.fasta.gz
hap1_hic_bam: s3://genomeark/species/Odontesthes_bonariensis/fOdoBon6/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fOdoBon6_hap1__s2.bam
hap2_hic_bam: s3://genomeark/species/Odontesthes_bonariensis/fOdoBon6/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fOdoBon6_hap2__s2.bam
hap1_pretext: s3://genomeark/species/Odontesthes_bonariensis/fOdoBon6/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fOdoBon6_hap1__s2_heatmap.pretext
hap2_pretext: s3://genomeark/species/Odontesthes_bonariensis/fOdoBon6/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fOdoBon6_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Odontesthes_bonariensis/fOdoBon6/assembly_vgp_HiC_2.0/evaluation/merqury/fOdoBon6_png/
pacbio_read_dir: s3://genomeark/species/Odontesthes_bonariensis/fOdoBon6/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Odontesthes_bonariensis/fOdoBon6/genomic_data/arima/
assembled_by_group: Rockefeller

pipeline:
  - hifiasm (0.16.1+galaxy3)
  - salsa (2.3+galaxy2)

notes: There was no Bionano data available. We are submitting hap1 for curation. Information for both hap1 and hap2 are listed here in case it would be useful.
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.