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 736.00 Gbp N/A 372.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 3 February 2026.
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 736.00 Gbp N/A 372.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 3 February 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 16 January 2026
fProLin1.hap1.cur.20260116.fasta.gz (381.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 23.36 Mbp 3 59.40 Mbp
20 14 15.01 Mbp 5 55.48 Mbp
30 25 11.70 Mbp 8 54.83 Mbp
40 40 8.82 Mbp 10 53.33 Mbp
50 60 6.00 Mbp 13 51.53 Mbp
60 94 3.26 Mbp 16 47.30 Mbp
70 154 1.87 Mbp 19 46.26 Mbp
80 263 1.00 Mbp 23 43.30 Mbp
90 490 404.60 Kbp 26 38.50 Mbp
100 1819 11.93 Kbp 811 11.93 Kbp
1.000x 1819 1.45 Gbp 811 1.45 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 16 January 2026
fProLin1.hap2.cur.20260116.fasta.gz (374.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 17.97 Mbp 3 57.34 Mbp
20 15 15.14 Mbp 5 53.43 Mbp
30 26 12.25 Mbp 8 51.81 Mbp
40 39 9.12 Mbp 11 50.61 Mbp
50 58 6.45 Mbp 13 48.75 Mbp
60 88 3.39 Mbp 16 46.22 Mbp
70 143 2.04 Mbp 20 44.09 Mbp
80 245 1.04 Mbp 23 42.96 Mbp
90 459 438.16 Kbp 26 36.83 Mbp
100 1537 14.39 Kbp 565 14.39 Kbp
1.000x 1537 1.42 Gbp 565 1.42 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.