Cyprinella lutrensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fCypLut1 47.02 Gbp N/A 34.4 GiB
PacBio HiFi (.bam) fCypLut1 141.47 Gbp N/A 487.1 GiB
Arima fCypLut1 106.14 Gbp N/A 55.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 October 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fCypLut1 PacBio HiFi (.fq) 47.02 Gbp N/A 34.4 GiB
PacBio HiFi (.bam) 141.47 Gbp N/A 487.1 GiB
Arima 106.14 Gbp N/A 55.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 October 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 20 October 2025
fCypLut1.hap1.cur.20251020.fasta.gz (219.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 11 6.03 Mbp 2 53.73 Mbp
20 31 3.44 Mbp 4 43.80 Mbp
30 73 1.79 Mbp 6 41.38 Mbp
40 133 1.39 Mbp 9 37.19 Mbp
50 206 1.16 Mbp 11 36.16 Mbp
60 293 1.00 Mbp 14 34.49 Mbp
70 394 0.84 Mbp 16 33.20 Mbp
80 516 0.69 Mbp 19 30.59 Mbp
90 668 0.52 Mbp 23 25.27 Mbp
100 1290 19.55 Kbp 455 19.55 Kbp
1.000x 1290 0.93 Gbp 455 0.93 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 27 October 2025
fCypLut1.hap2.cur.20251027.fasta.gz (213.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 12 5.21 Mbp 2 53.13 Mbp
20 37 2.44 Mbp 4 41.75 Mbp
30 84 1.70 Mbp 6 39.13 Mbp
40 144 1.35 Mbp 9 37.19 Mbp
50 216 1.14 Mbp 11 34.82 Mbp
60 301 0.98 Mbp 14 33.14 Mbp
70 400 0.83 Mbp 16 30.92 Mbp
80 516 0.69 Mbp 19 29.36 Mbp
90 663 0.52 Mbp 23 24.94 Mbp
100 1211 15.60 Kbp 390 15.60 Kbp
1.000x 1211 0.89 Gbp 390 0.89 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 December 2023
fCypLut1.MT.20231215.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fCypLut1.yml (view)
species: Cyprinella lutrensis
specimen: fCypLut1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
hap1: s3://genomeark/species/Cyprinella_lutrensis/fCypLut1/assembly_vgp_HiC_2.0/fCypLut1.HiC.hap1.20231215.fasta.gz
hap2: s3://genomeark/species/Cyprinella_lutrensis/fCypLut1/assembly_vgp_HiC_2.0/fCypLut1.HiC.hap2.20231215.fasta.gz
pretext_hap1: s3://genomeark/species/Cyprinella_lutrensis/fCypLut1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fCypLut1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Cyprinella_lutrensis/fCypLut1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fCypLut1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Cyprinella_lutrensis/fCypLut1/assembly_vgp_HiC_2.0/evaluation/merqury_postpurge/fCypLut1_png/
pacbio_read_dir: s3://genomeark/species/Cyprinella_lutrensis/fCypLut1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Cyprinella_lutrensis/fCypLut1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fCypLut1, resulting in two complete haplotypes. These haplotypes underwent purge_dups. HiC scaffolding was performed with YaHS. The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. This sample did not have bionano data. This sample needed to have purging performed on the contigs, before scaffolding. 
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.