Prochilodus lineatus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fProLin1 66.32 Gbp N/A 34.7 GiB
PacBio HiFi (.bam) fProLin1 66.79 Gbp N/A 263.8 GiB
Arima fProLin1 362.32 Gbp N/A 194.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 April 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fProLin1 PacBio HiFi (.fq) 66.32 Gbp N/A 34.7 GiB
PacBio HiFi (.bam) 66.79 Gbp N/A 263.8 GiB
Arima 362.32 Gbp N/A 194.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 April 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 13 July 2024
fProLin1.HiC.hap1.20240713.fasta.gz (378.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 21.71 Mbp 3 57.34 Mbp
20 14 15.35 Mbp 5 52.80 Mbp
30 25 11.89 Mbp 8 49.58 Mbp
40 39 8.82 Mbp 11 48.85 Mbp
50 59 6.19 Mbp 14 47.30 Mbp
60 91 3.35 Mbp 17 44.14 Mbp
70 148 1.97 Mbp 20 43.38 Mbp
80 254 0.99 Mbp 24 36.16 Mbp
90 481 400.10 Kbp 30 12.16 Mbp
100 1820 11.93 Kbp 854 11.93 Kbp
1.000x 1820 1.43 Gbp 854 1.43 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 13 July 2024
fProLin1.HiC.hap2.20240713.fasta.gz (378.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 20.38 Mbp 3 59.21 Mbp
20 15 15.01 Mbp 5 55.10 Mbp
30 26 11.77 Mbp 8 51.53 Mbp
40 40 8.94 Mbp 11 49.13 Mbp
50 59 6.32 Mbp 14 46.20 Mbp
60 91 3.34 Mbp 17 43.95 Mbp
70 149 1.93 Mbp 20 42.59 Mbp
80 253 1.05 Mbp 24 36.19 Mbp
90 466 441.82 Kbp 30 9.58 Mbp
100 1536 14.39 Kbp 590 14.39 Kbp
1.000x 1536 1.44 Gbp 590 1.44 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 July 2024
fProLin1.MT.20240715.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fProLin1.yml (view)
species: Prochilodus lineatus
specimen: fProLin1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Prochilodus_lineatus/fProLin1/assembly_vgp_HiC_2.0/fProLin1.HiC.hap1.20240713.fasta.gz
hap2: s3://genomeark/species/Prochilodus_lineatus/fProLin1/assembly_vgp_HiC_2.0/fProLin1.HiC.hap2.20240713.fasta.gz
pretext_hap1: s3://genomeark/species/Prochilodus_lineatus/fProLin1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fProLin1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Prochilodus_lineatus/fProLin1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fProLin1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Prochilodus_lineatus/fProLin1/assembly_vgp_HiC_2.0/evaluation/merqury/hap1_purged/fProLin1_png/
mito: s3://genomeark/species/Prochilodus_lineatus/fProLin1/assembly_MT_rockefeller/fProLin1.MT.20240715.fasta.gz
pacbio_read_dir: s3://genomeark/species/Prochilodus_lineatus/fProLin1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Prochilodus_lineatus/fProLin1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fProLin1, resulting in two complete haplotypes. The HiC prep kit used was Arima, so the HiC reads require trimming 5 bp off the 5' end. The assembly was performed on the Rockefeller University VGL instance. The merqury plots for the contigs indicate potential duplicates in both haplotypes, but I was unable to remove this signal with purge_dups even with custom cutoffs. 
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.