Cyprinella venusta

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) fCypVen1 1300.09 Gbp N/A 2.2 TiB
PacBio HiFi (.fq) fCypVen1 48.59 Gbp N/A 29.9 GiB
PacBio HiFi (.bam) fCypVen1 151.64 Gbp N/A 505.5 GiB
Arima fCypVen1 68.46 Gbp N/A 35.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fCypVen1 PacBio HiFi (subreads) 1300.09 Gbp N/A 2.2 TiB
PacBio HiFi (.fq) 48.59 Gbp N/A 29.9 GiB
PacBio HiFi (.bam) 151.64 Gbp N/A 505.5 GiB
Arima 68.46 Gbp N/A 35.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 21 April 2024
fCypVen1.hap1.cur.20240421.fasta.gz (238.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 10 7.28 Mbp 2 55.99 Mbp
20 27 4.09 Mbp 4 42.85 Mbp
30 55 2.87 Mbp 6 38.41 Mbp
40 95 1.97 Mbp 9 36.89 Mbp
50 148 1.53 Mbp 11 35.36 Mbp
60 214 1.29 Mbp 14 34.04 Mbp
70 294 1.04 Mbp 17 31.57 Mbp
80 394 0.81 Mbp 20 29.44 Mbp
90 525 0.58 Mbp 23 24.84 Mbp
100 1382 150 bp 673 12.20 Kbp
1.000x 1382 0.92 Gbp 673 0.92 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 21 April 2024
fCypVen1.hap2.cur.20240421.fasta.gz (214.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 11 6.35 Mbp 2 56.08 Mbp
20 31 3.71 Mbp 4 44.69 Mbp
30 63 2.38 Mbp 6 39.20 Mbp
40 106 1.95 Mbp 9 37.59 Mbp
50 160 1.55 Mbp 11 35.22 Mbp
60 225 1.31 Mbp 14 34.29 Mbp
70 304 1.07 Mbp 17 31.15 Mbp
80 403 0.83 Mbp 20 29.87 Mbp
90 532 0.61 Mbp 23 27.97 Mbp
100 1132 163 bp 412 13.51 Kbp
1.000x 1132 0.93 Gbp 412 0.93 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 June 2023
fCypVen1.MT.20230617.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fCypVen1.yml (view)
species: Cyprinella venusta
specimen: fCypVen1
projects: 
  - vgp
hap1: s3://genomeark/species/Cyprinella_venusta/fCypVen1/assembly_vgp_HiC_2.0/fCypVen1.HiC.hap1.20230613.fasta.gz
hap2: s3://genomeark/species/Cyprinella_venusta/fCypVen1/assembly_vgp_HiC_2.0/fCypVen1.HiC.hap2.20230613.fasta.gz
pretext_hap1: s3://genomeark/species/Cyprinella_venusta/fCypVen1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fCypVen1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Cyprinella_venusta/fCypVen1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fCypVen1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Cyprinella_venusta/fCypVen1/assembly_vgp_HiC_2.0/evaluation/purge_dups/merqury/fCypVen1_png/
mito: s3://genomeark/species/Cyprinella_venusta/fCypVen1/assembly_MT_rockefeller/fCypVen1.MT.20230617.fasta.gz
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of fCypVen1, resulting in two complete haplotypes. This individual did have not bionano data. The hap1 and hap2 assemblies were purged with the purge_dups piepeline. 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.