Salminus brasiliensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fSalBra1 40.53 Gbp N/A 32.1 GiB
Arima fSalBra1 111.25 Gbp N/A 57.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 January 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fSalBra1 PacBio HiFi (.fq) 40.53 Gbp N/A 32.1 GiB
Arima 111.25 Gbp N/A 57.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 January 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 12 May 2023
fSalBra1.hap1.decon.20230512.fasta.gz (285.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 20.16 Mbp 2 60.83 Mbp
20 11 15.38 Mbp 4 47.62 Mbp
30 19 12.10 Mbp 6 44.64 Mbp
40 29 8.44 Mbp 8 43.70 Mbp
50 44 6.14 Mbp 11 38.93 Mbp
60 65 3.96 Mbp 14 36.16 Mbp
70 97 2.64 Mbp 17 35.01 Mbp
80 150 1.58 Mbp 20 34.17 Mbp
90 260 0.61 Mbp 23 29.94 Mbp
100 823 16.36 Kbp 182 16.36 Kbp
1.000x 823 1.06 Gbp 182 1.08 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 12 May 2023
fSalBra1.hap2.cur.20230512.fasta.gz (285.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 17.17 Mbp 2 60.49 Mbp
20 13 13.94 Mbp 4 50.28 Mbp
30 21 11.72 Mbp 6 46.42 Mbp
40 32 8.06 Mbp 8 43.35 Mbp
50 47 5.83 Mbp 11 40.77 Mbp
60 68 4.15 Mbp 13 38.87 Mbp
70 99 2.77 Mbp 16 36.84 Mbp
80 148 1.61 Mbp 19 36.20 Mbp
90 250 0.64 Mbp 22 33.96 Mbp
100 829 19.03 Kbp 103 19.03 Kbp
1.000x 829 1.06 Gbp 103 1.07 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 February 2023
fSalBra1.MT.20230210.fasta.gz (5.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fSalBra1_hap2.yml (view)
species: Salminus brasiliensis
specimen: fSalBra1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Salminus_brasiliensis/fSalBra1/assembly_vgp_HiC_2.0/fSalBra1.HiC.hap1.20230305.fasta.gz
hap2: s3://genomeark/species/Salminus_brasiliensis/fSalBra1/assembly_vgp_HiC_2.0/fSalBra1.HiC.hap2.20230305.fasta.gz
pretext_hap1: s3://genomeark/species/Salminus_brasiliensis/fSalBra1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fSalBra1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Salminus_brasiliensis/fSalBra1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fSalBra1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Salminus_brasiliensis/fSalBra1/assembly_vgp_HiC_2.0/evaluation/merqury/fSalBra1_png/
mito: s3://genomeark/species/Salminus_brasiliensis/fSalBra1/assembly_MT_rockefeller/fSalBra1.MT.20230210.fasta.gz
pacbio_read_dir: s3://genomeark/species/Salminus_brasiliensis/fSalBra1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Salminus_brasiliensis/fSalBra1/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Salminus_brasiliensis/fSalBra1/genomic_data/bionano/
pipeline:
  - hifiasm (0.16.1+galaxy4)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of fSalBra1, resulting in two complete haplotypes. This individual had 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 hap2 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.