Fejervarya limnocharis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aFejLim2 228.54 Gbp N/A 103.9 GiB
PacBio HiFi (.bam) aFejLim2 233.35 Gbp N/A 757.2 GiB
Arima aFejLim1 313.76 Gbp N/A 166.0 GiB
aFejLim2 348.61 Gbp N/A 183.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aFejLim1 Arima 313.76 Gbp N/A 166.0 GiB
aFejLim2 PacBio HiFi (.fq) 228.54 Gbp N/A 103.9 GiB
PacBio HiFi (.bam) 233.35 Gbp N/A 757.2 GiB
Arima 348.61 Gbp N/A 183.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 June 2025.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 2 December 2025
aFejLim2.hap1.cur.20251202.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 24 13.42 Mbp 1 0.55 Gbp
20 56 9.30 Mbp 2 441.80 Mbp
30 100 7.04 Mbp 3 391.82 Mbp
40 158 5.48 Mbp 4 390.09 Mbp
50 228 4.51 Mbp 4 390.09 Mbp
60 318 3.48 Mbp 5 352.21 Mbp
70 430 2.78 Mbp 7 199.05 Mbp
80 582 1.93 Mbp 9 173.68 Mbp
90 821 1.08 Mbp 11 152.37 Mbp
100 2314 8.48 Kbp 629 8.48 Kbp
1.000x 2314 3.52 Gbp 629 3.52 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 2 December 2025
aFejLim2.hap2.cur.20251202.fasta.gz (850.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 22 11.91 Mbp 1 0.54 Gbp
20 57 8.72 Mbp 2 439.60 Mbp
30 102 6.96 Mbp 3 394.17 Mbp
40 157 5.82 Mbp 4 385.64 Mbp
50 223 4.77 Mbp 4 385.64 Mbp
60 306 3.82 Mbp 5 352.23 Mbp
70 410 2.88 Mbp 7 197.45 Mbp
80 554 1.98 Mbp 9 175.87 Mbp
90 781 1.15 Mbp 11 151.83 Mbp
100 1979 9.80 Kbp 315 9.80 Kbp
1.000x 1979 3.49 Gbp 315 3.49 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 21 August 2025
aFejLim2.MT.20250821.fasta.gz (5.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/aFejLim2.yml (view)
species: Fejervarya limnocharis
specimem: aFejLim2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Fejervarya_limnocharis/aFejLim2/assembly_vgp_HiC_2.0/aFejLim2.HiC.hap1.20250822.fasta.gz
hap2: s3://genomeark/species/Fejervarya_limnocharis/aFejLim2/assembly_vgp_HiC_2.0/aFejLim2.HiC.hap2.20250822.fasta.gz
pretext_hap1: s3://genomeark/species/Fejervarya_limnocharis/aFejLim2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/aFejLim2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Fejervarya_limnocharis/aFejLim2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/aFejLim2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Fejervarya_limnocharis/aFejLim2/assembly_vgp_HiC_2.0/evaluation/merqury/aFejLim2_png/
pacbio_read_dir: s3://genomeark/species/Fejervarya_limnocharis/aFejLim2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Fejervarya_limnocharis/aFejLim2/genomic_data/arima/
pipeline:
  - hifiasm (v0.25.0+galaxy0)
  - yahs (v1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.1)
  - VGP1 genomic profiling workflow (v0.3)
  - VGP4 HiFi HiC assembly workflow (v0.3.8)
  - VGP8 HiC scaffolding workflow (v2.0)
  - VGP9 decontamination workflow (kraken2 v2.1.3+galaxy1) with database PlusPF 2022 and filtering scaffolds >1 billion base pairs to avoid blast crushing
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm-HiC assembly of aFejLim2 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.