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_curated from 13 May 2026
fAplLin1.hap1.cur.20260513.fasta.gz (157.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 27.09 Mbp 2 30.85 Mbp
20 5 26.46 Mbp 4 28.84 Mbp
30 7 23.89 Mbp 7 28.11 Mbp
40 10 22.94 Mbp 9 26.32 Mbp
50 13 18.54 Mbp 11 25.23 Mbp
60 16 17.46 Mbp 13 24.27 Mbp
70 20 12.47 Mbp 16 23.64 Mbp
80 25 10.70 Mbp 19 20.66 Mbp
90 34 4.45 Mbp 21 20.29 Mbp
100 106 18.03 Kbp 32 18.03 Kbp
1.000x 106 0.60 Gbp 32 0.60 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 13 May 2026
fAplLin1.hap2.cur.20260513.fasta.gz (153.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 25.76 Mbp 2 29.22 Mbp
20 5 25.43 Mbp 4 26.73 Mbp
30 7 23.31 Mbp 7 25.95 Mbp
40 9 23.11 Mbp 9 25.66 Mbp
50 12 20.61 Mbp 11 24.30 Mbp
60 15 19.64 Mbp 13 23.62 Mbp
70 18 17.40 Mbp 16 20.86 Mbp
80 21 14.96 Mbp 18 20.20 Mbp
90 26 5.45 Mbp 21 18.54 Mbp
100 78 20.95 Kbp 28 20.95 Kbp
1.000x 78 0.56 Gbp 28 0.56 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.