Haplochromis burtoni

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fHapBur1 36.33 Gbp N/A 25.2 GiB
fHapBur2 37.16 Gbp N/A 32.8 GiB
Arima fHapBur1 103.05 Gbp N/A 48.9 GiB
fHapBur2 55.63 Gbp N/A 27.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fHapBur1 PacBio HiFi (.fq) 36.33 Gbp N/A 25.2 GiB
Arima 103.05 Gbp N/A 48.9 GiB
fHapBur2 PacBio HiFi (.fq) 37.16 Gbp N/A 32.8 GiB
Arima 55.63 Gbp N/A 27.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 17 June 2023
fHapBur1.hap1.decontam.20230617.fasta.gz (233.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 20.30 Mbp 1 113.41 Mbp
20 10 15.39 Mbp 2 75.39 Mbp
30 16 12.71 Mbp 4 64.25 Mbp
40 23 10.43 Mbp 5 58.98 Mbp
50 33 8.60 Mbp 7 40.57 Mbp
60 44 6.50 Mbp 9 38.81 Mbp
70 59 5.09 Mbp 11 35.80 Mbp
80 78 3.75 Mbp 14 32.48 Mbp
90 109 2.07 Mbp 17 25.66 Mbp
100 396 11.46 Kbp 217 11.46 Kbp
1.000x 396 0.88 Gbp 217 0.88 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 17 June 2023
fHapBur1.hap2.decontam.20230617.fasta.gz (237.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 25.37 Mbp 1 114.80 Mbp
20 8 20.82 Mbp 2 66.72 Mbp
30 13 14.33 Mbp 4 61.91 Mbp
40 19 12.52 Mbp 5 60.66 Mbp
50 28 9.13 Mbp 7 46.59 Mbp
60 39 7.39 Mbp 9 40.64 Mbp
70 53 5.63 Mbp 12 37.50 Mbp
80 72 4.06 Mbp 14 35.51 Mbp
90 101 2.22 Mbp 17 24.01 Mbp
100 387 12.51 Kbp 231 12.51 Kbp
1.000x 387 0.90 Gbp 231 0.90 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 5 January 2024
fHapBur1.MT.20240105.fasta.gz (5.4 KiB)

Quality: not computed
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 15 June 2023
fHapBur2.hap1.decontam.20230615.fasta.gz (237.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 25.54 Mbp 2 68.25 Mbp
20 8 18.40 Mbp 3 66.04 Mbp
30 13 14.57 Mbp 4 64.91 Mbp
40 20 11.95 Mbp 6 47.78 Mbp
50 28 9.77 Mbp 8 40.64 Mbp
60 38 8.34 Mbp 11 38.09 Mbp
70 50 6.60 Mbp 13 36.32 Mbp
80 67 4.59 Mbp 15 35.05 Mbp
90 93 2.42 Mbp 18 32.40 Mbp
100 339 14.85 Kbp 201 14.85 Kbp
1.000x 339 0.90 Gbp 201 0.90 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 15 June 2023
fHapBur2.hap2.decontam.20230615.fasta.gz (235.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 29.99 Mbp 1 111.73 Mbp
20 6 21.51 Mbp 2 77.46 Mbp
30 10 17.62 Mbp 4 65.02 Mbp
40 16 15.20 Mbp 5 55.64 Mbp
50 22 13.65 Mbp 7 46.28 Mbp
60 30 9.16 Mbp 9 41.63 Mbp
70 42 6.59 Mbp 11 38.08 Mbp
80 58 4.68 Mbp 14 33.76 Mbp
90 81 2.91 Mbp 16 32.57 Mbp
100 250 21.63 Kbp 128 21.63 Kbp
1.000x 250 0.89 Gbp 128 0.89 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 June 2023
fHapBur2.MT.20230615.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fHapBur1.yml (view)
species: Haplochromis burtoni
specimen: fHapBur1
projects: 
  - vgp
hap1: s3://genomeark/species/Haplochromis_burtoni/fHapBur1/assembly_vgp_HiC_2.0/fHapBur1.HiC.hap1.20230617.fasta.gz
hap2: s3://genomeark/species/Haplochromis_burtoni/fHapBur1/assembly_vgp_HiC_2.0/fHapBur1.HiC.hap2.20230617.fasta.gz
pretext_hap1: s3://genomeark/species/Haplochromis_burtoni/fHapBur1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fHapBur1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Haplochromis_burtoni/fHapBur1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fHapBur1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Haplochromis_burtoni/fHapBur1/assembly_vgp_HiC_2.0/evaluation/merqury/fHapBur1_png/
mito: s3://genomeark/species/Haplochromis_burtoni/fHapBur1/assembly_MT_rockefeller/fHapBur1.MT.20230617.fasta.gz
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of fHapBur1, resulting in two complete haplotypes. This individual did have not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2.
assembly_vgp_HiC_2.0/fHapBur2.yml (view)
species: Haplochromis burtoni
specimen: fHapBur2
projects: 
  - vgp
hap1: s3://genomeark/species/Haplochromis_burtoni/fHapBur2/assembly_vgp_HiC_2.0/fHapBur2.HiC.hap1.20230615.fasta.gz
hap2: s3://genomeark/species/Haplochromis_burtoni/fHapBur2/assembly_vgp_HiC_2.0/fHapBur2.HiC.hap2.20230615.fasta.gz
pretext_hap1: s3://genomeark/species/Haplochromis_burtoni/fHapBur2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fHapBur2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Haplochromis_burtoni/fHapBur2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fHapBur2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Haplochromis_burtoni/fHapBur2/assembly_vgp_HiC_2.0/evaluation/merqury/fHapBur2_png/
mito: s3://genomeark/species/Haplochromis_burtoni/fHapBur2/assembly_MT_rockefeller/fHapBur2.MT.20230615.fasta.gz
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of fHapBur2, resulting in two complete haplotypes. This individual did have not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2.
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.