Aplocheilus lineatus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fAplLin1 77.78 Gbp N/A 34.6 GiB
PacBio HiFi (.bam) fAplLin1 81.86 Gbp N/A 269.6 GiB
Arima fAplLin1 50.02 Gbp N/A 26.9 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
fAplLin1 PacBio HiFi (.fq) 77.78 Gbp N/A 34.6 GiB
PacBio HiFi (.bam) 81.86 Gbp N/A 269.6 GiB
Arima 50.02 Gbp N/A 26.9 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 14 October 2025
fAplLin1.HiC.hap1.20251014.fasta.gz (147.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 27.09 Mbp 2 40.73 Mbp
20 5 25.76 Mbp 3 39.63 Mbp
30 7 23.89 Mbp 5 30.63 Mbp
40 10 20.61 Mbp 7 28.12 Mbp
50 13 20.01 Mbp 10 26.73 Mbp
60 16 18.54 Mbp 12 25.95 Mbp
70 20 16.07 Mbp 14 23.89 Mbp
80 24 10.70 Mbp 17 22.52 Mbp
90 35 2.79 Mbp 20 20.34 Mbp
100 310 6.19 Kbp 237 6.19 Kbp
1.000x 310 0.61 Gbp 237 0.61 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 14 October 2025
fAplLin1.HiC.hap2.20251014.fasta.gz (143.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 26.46 Mbp 2 48.65 Mbp
20 5 25.43 Mbp 3 33.51 Mbp
30 7 23.62 Mbp 5 28.84 Mbp
40 10 23.17 Mbp 7 26.07 Mbp
50 12 22.93 Mbp 9 25.66 Mbp
60 15 17.46 Mbp 11 24.30 Mbp
70 19 15.63 Mbp 14 23.62 Mbp
80 23 11.22 Mbp 16 19.61 Mbp
90 29 5.06 Mbp 19 18.54 Mbp
100 135 9.25 Kbp 77 9.25 Kbp
1.000x 135 0.58 Gbp 77 0.58 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 October 2025
fAplLin1.MT.20251013.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fAplLin1.yml (view)
species: Aplocheilus lineatus
specimem: fAplLin1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Aplocheilus_lineatus/fAplLin1/assembly_vgp_HiC_2.0/fAplLin1.HiC.hap1.20251014.fasta.gz
hap2: s3://genomeark/species/Aplocheilus_lineatus/fAplLin1/assembly_vgp_HiC_2.0/fAplLin1.HiC.hap2.20251014.fasta.gz
pretext_hap1: s3://genomeark/species/Aplocheilus_lineatus/fAplLin1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/fAplLin1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Aplocheilus_lineatus/fAplLin1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/fAplLin1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Aplocheilus_lineatus/fAplLin1/assembly_vgp_HiC_2.0/evaluation/merqury/fAplLin1_png/
pacbio_read_dir: s3://genomeark/species/Aplocheilus_lineatus/fAplLin1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Aplocheilus_lineatus/fAplLin1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v3.1) with mapq=10
  - VGP9 decontamination workflow (v1.0) 
  - VGP6 purge dups workflow (v0.10.4)
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of fAplLin1 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. 
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.