Salvelinus alpinus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fSalAlp3 104.20 Gbp N/A 61.6 GiB
PacBio HiFi (.bam) fSalAlp3 51.08 Gbp N/A 204.6 GiB
Arima fSalAlp3 238.05 Gbp N/A 121.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 1 August 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fSalAlp3 PacBio HiFi (.fq) 104.20 Gbp N/A 61.6 GiB
PacBio HiFi (.bam) 51.08 Gbp N/A 204.6 GiB
Arima 238.05 Gbp N/A 121.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 1 August 2023.
Assemblies
Individual 3 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 13 September 2023
fSalAlp3.HiC.hap1.20230913.fasta.gz (577.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 41 4.32 Mbp 3 108.28 Mbp
20 107 2.84 Mbp 5 92.62 Mbp
30 201 2.03 Mbp 8 70.95 Mbp
40 333 1.47 Mbp 11 62.68 Mbp
50 520 1.03 Mbp 15 57.60 Mbp
60 785 0.72 Mbp 19 51.92 Mbp
70 1161 0.51 Mbp 23 48.54 Mbp
80 1731 315.37 Kbp 28 41.98 Mbp
90 2729 161.04 Kbp 83 0.97 Mbp
100 5877 10.18 Kbp 1724 10.18 Kbp
1.000x 5877 2.27 Gbp 1724 2.27 Gbp
NG based on genome size .
Individual 3 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 13 September 2023
fSalAlp3.HiC.hap2.20230913.fasta.gz (522.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 39 3.93 Mbp 3 83.97 Mbp
20 104 2.57 Mbp 5 67.56 Mbp
30 194 1.90 Mbp 9 50.49 Mbp
40 320 1.34 Mbp 13 45.54 Mbp
50 501 0.91 Mbp 17 41.53 Mbp
60 763 0.64 Mbp 22 37.85 Mbp
70 1155 414.04 Kbp 28 33.80 Mbp
80 1767 261.27 Kbp 35 17.45 Mbp
90 2831 129.18 Kbp 194 483.74 Kbp
100 6075 4.37 Kbp 2187 4.37 Kbp
1.000x 6075 2.00 Gbp 2187 2.01 Gbp
NG based on genome size .
Individual 3 Mitochondrial Assembly
Version assembly_MT_rockefeller from 14 September 2023
fSalAlp3.MT.20230914.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fSalAlp3_hap1.yml (view)
species: Salvelinus alpinus
specimen: fSalAlp3
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap1.20230829.fasta.gz
hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap2.20230829.fasta.gz
pretext_hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fSalAlp3_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fSalAlp3_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/merqury/fSalAlp3_png/
pacbio_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/arima/
mito: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_MT_rockefeller/fSalAlp3.MT.20230914.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fSalAlp3, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT. 
assembly_vgp_HiC_2.0/fSalAlp3_hap2.yml (view)
species: Salvelinus alpinus
specimen: fSalAlp3
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap1.20230913.fasta.gz
hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap2.20230913.fasta.gz
pretext_hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fSalAlp3_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fSalAlp3_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/merqury/fSalAlp3_png/
pacbio_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/arima/
mito: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_MT_rockefeller/fSalAlp3.MT.20230913.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fSalAlp3, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT. 

species: Salvelinus alpinus
specimen: fSalAlp3
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap1.20230829.fasta.gz
hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap2.20230829.fasta.gz
pretext_hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fSalAlp3_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fSalAlp3_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/merqury/fSalAlp3_png/
pacbio_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/arima/
mito: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_MT_rockefeller/fSalAlp3.MT.20230914.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fSalAlp3, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT. 
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.