Nematolebias whitei

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fNemWhi1 118.57 Gbp N/A 52.7 GiB
PacBio HiFi (.bam) fNemWhi1 120.20 Gbp N/A 391.1 GiB
Arima fNemWhi1 73.14 Gbp N/A 40.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fNemWhi1 PacBio HiFi (.fq) 118.57 Gbp N/A 52.7 GiB
PacBio HiFi (.bam) 120.20 Gbp N/A 391.1 GiB
Arima 73.14 Gbp N/A 40.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 July 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 16 October 2025
fNemWhi1.HiC.hap1.20251016.fasta.gz (355.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 25.57 Mbp 2 114.37 Mbp
20 12 20.12 Mbp 3 106.93 Mbp
30 20 13.49 Mbp 4 94.59 Mbp
40 32 10.30 Mbp 6 68.78 Mbp
50 48 8.09 Mbp 9 59.38 Mbp
60 67 6.52 Mbp 11 58.00 Mbp
70 93 4.70 Mbp 14 48.66 Mbp
80 131 3.01 Mbp 16 48.17 Mbp
90 193 1.71 Mbp 20 32.46 Mbp
100 788 15.47 Kbp 450 15.47 Kbp
1.000x 788 1.41 Gbp 450 1.41 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 16 October 2025
fNemWhi1.HiC.hap2.20251016.fasta.gz (355.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 25.49 Mbp 1 165.63 Mbp
20 11 20.31 Mbp 3 71.32 Mbp
30 19 16.16 Mbp 5 68.06 Mbp
40 30 12.25 Mbp 7 61.70 Mbp
50 43 9.16 Mbp 9 58.68 Mbp
60 62 6.85 Mbp 11 57.63 Mbp
70 86 4.95 Mbp 14 52.58 Mbp
80 121 3.30 Mbp 17 47.00 Mbp
90 177 1.86 Mbp 21 30.82 Mbp
100 594 16.85 Kbp 286 16.85 Kbp
1.000x 594 1.41 Gbp 286 1.41 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/fNemWhi1.yml (view)
species: Nematolebias whitei
specimem: fNemWhi1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Nematolebias_whitei/fNemWhi1/assembly_vgp_HiC_2.0/fNemWhi1.HiC.hap1.20251016.fasta.gz
hap2: s3://genomeark/species/Nematolebias_whitei/fNemWhi1/assembly_vgp_HiC_2.0/fNemWhi1.HiC.hap2.20251016.fasta.gz
pretext_hap1: s3://genomeark/species/Nematolebias_whitei/fNemWhi1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fNemWhi1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Nematolebias_whitei/fNemWhi1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fNemWhi1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Nematolebias_whitei/fNemWhi1/assembly_vgp_HiC_2.0/evaluation/merqury/fNemWhi1_png/
pacbio_read_dir: s3://genomeark/species/Nematolebias_whitei/fNemWhi1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Nematolebias_whitei/fNemWhi1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP1 genomic profiling workflow (v0.2.2)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow (v1.1) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fNemWhi1 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA. Mitogenome was not assembled in mitoHiFi as no HiFi reads were mapped to the mito reference. There are some 2-copy k-mers in the diploid coverage range in hap2. I injected a track in pretextmap to show the location of the potential haplotigs/overlaps identified by purge-dups tool. Curation team could use the track to assess whether they are real haplotigs (note that purge_dups tool tends to over-purge).
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.