Rivulus cylindraceus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fRivCyl1 96.45 Gbp N/A 42.5 GiB
PacBio HiFi (.bam) fRivCyl1 100.66 Gbp N/A 327.3 GiB
Arima fRivCyl1 78.41 Gbp N/A 42.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fRivCyl1 PacBio HiFi (.fq) 96.45 Gbp N/A 42.5 GiB
PacBio HiFi (.bam) 100.66 Gbp N/A 327.3 GiB
Arima 78.41 Gbp N/A 42.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 3 October 2025
fRivCyl1.HiC.hap1.20251003.fasta.gz (171.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 32.15 Mbp 2 33.35 Mbp
20 4 29.85 Mbp 4 31.44 Mbp
30 7 29.01 Mbp 6 30.39 Mbp
40 9 27.28 Mbp 9 29.01 Mbp
50 12 24.14 Mbp 11 27.50 Mbp
60 14 22.92 Mbp 13 26.53 Mbp
70 18 19.82 Mbp 16 23.66 Mbp
80 21 17.16 Mbp 19 22.19 Mbp
90 26 8.75 Mbp 22 20.17 Mbp
100 321 7.02 Kbp 288 7.02 Kbp
1.000x 321 0.65 Gbp 288 0.66 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 3 October 2025
fRivCyl1.HiC.hap2.20251003.fasta.gz (172.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 32.79 Mbp 2 34.19 Mbp
20 4 31.43 Mbp 4 31.98 Mbp
30 7 30.21 Mbp 6 30.60 Mbp
40 9 28.11 Mbp 9 29.60 Mbp
50 11 27.59 Mbp 11 28.11 Mbp
60 14 25.73 Mbp 13 27.53 Mbp
70 16 24.78 Mbp 16 25.33 Mbp
80 20 18.90 Mbp 19 23.31 Mbp
90 23 13.57 Mbp 22 20.81 Mbp
100 128 11.22 Kbp 118 11.22 Kbp
1.000x 128 0.67 Gbp 118 0.67 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 3 October 2025
fRivCyl1.MT.20251003.fasta.gz (5.6 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fRivCyl1.yml (view)
species: Rivulus cylindraceus
specimem: fRivCyl1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Rivulus_cylindraceus/fRivCyl1/assembly_vgp_HiC_2.0/fRivCyl1.HiC.hap1.20251003.fasta.gz
hap2: s3://genomeark/species/Rivulus_cylindraceus/fRivCyl1/assembly_vgp_HiC_2.0/fRivCyl1.HiC.hap2.20251003.fasta.gz
pretext_hap1: s3://genomeark/species/Rivulus_cylindraceus/fRivCyl1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fRivCyl1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Rivulus_cylindraceus/fRivCyl1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fRivCyl1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Rivulus_cylindraceus/fRivCyl1/assembly_vgp_HiC_2.0/evaluation/merqury/fRivCyl1_png/
pacbio_read_dir: s3://genomeark/species/Rivulus_cylindraceus/fRivCyl1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Rivulus_cylindraceus/fRivCyl1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fRivCyl1 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.