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
Arima fCypLut1 106.14 Gbp N/A 55.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 July 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fCypLut1 PacBio HiFi (.fq) 47.02 Gbp N/A 34.4 GiB
Arima 106.14 Gbp N/A 55.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 July 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 15 December 2023
fCypLut1.HiC.hap1.20231215.fasta.gz (239.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 12 5.71 Mbp 2 67.58 Mbp
20 35 2.80 Mbp 3 62.31 Mbp
30 79 1.77 Mbp 5 41.45 Mbp
40 138 1.38 Mbp 7 38.13 Mbp
50 210 1.16 Mbp 9 36.46 Mbp
60 295 0.99 Mbp 12 33.76 Mbp
70 394 0.85 Mbp 15 32.07 Mbp
80 511 0.70 Mbp 17 30.37 Mbp
90 659 0.53 Mbp 21 24.81 Mbp
100 1265 18.63 Kbp 472 18.63 Kbp
1.000x 1265 0.91 Gbp 472 0.91 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 15 December 2023
fCypLut1.HiC.hap2.20231215.fasta.gz (241.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 11 6.03 Mbp 2 52.14 Mbp
20 32 3.06 Mbp 3 49.29 Mbp
30 76 1.75 Mbp 5 42.38 Mbp
40 136 1.40 Mbp 8 37.51 Mbp
50 208 1.17 Mbp 10 36.16 Mbp
60 292 1.01 Mbp 13 33.20 Mbp
70 391 0.85 Mbp 16 30.92 Mbp
80 509 0.70 Mbp 19 28.57 Mbp
90 656 0.53 Mbp 22 23.84 Mbp
100 1208 15.60 Kbp 408 15.60 Kbp
1.000x 1208 0.91 Gbp 408 0.91 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.