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_vgp_HiC_2.0 from 22 August 2025
aFejLim2.HiC.hap1.20250822.fasta.gz (861.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 24 11.97 Mbp 1 0.93 Gbp
20 59 8.81 Mbp 1 0.93 Gbp
30 104 6.87 Mbp 2 441.80 Mbp
40 163 5.52 Mbp 3 386.28 Mbp
50 233 4.55 Mbp 4 350.55 Mbp
60 323 3.48 Mbp 5 200.84 Mbp
70 435 2.81 Mbp 6 199.27 Mbp
80 587 1.90 Mbp 8 173.68 Mbp
90 831 1.07 Mbp 10 151.33 Mbp
100 2553 8.48 Kbp 900 8.48 Kbp
1.000x 2553 3.53 Gbp 900 3.53 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 22 August 2025
aFejLim2.HiC.hap2.20250822.fasta.gz (849.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 22 13.60 Mbp 1 1.40 Gbp
20 54 8.94 Mbp 1 1.40 Gbp
30 97 7.19 Mbp 1 1.40 Gbp
40 151 5.90 Mbp 1 1.40 Gbp
50 217 4.75 Mbp 2 362.35 Mbp
60 299 3.84 Mbp 3 352.21 Mbp
70 403 2.86 Mbp 5 190.48 Mbp
80 549 2.01 Mbp 7 175.87 Mbp
90 773 1.17 Mbp 9 151.83 Mbp
100 2017 9.80 Kbp 394 9.80 Kbp
1.000x 2017 3.49 Gbp 394 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.