Lestoros inca

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mLesInc1 217.93 Gbp N/A 97.6 GiB
PacBio HiFi (.bam) mLesInc1 222.62 Gbp N/A 716.4 GiB
Arima mLesInc1 280.06 Gbp N/A 145.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 June 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mLesInc1 PacBio HiFi (.fq) 217.93 Gbp N/A 97.6 GiB
PacBio HiFi (.bam) 222.62 Gbp N/A 716.4 GiB
Arima 280.06 Gbp N/A 145.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 10 June 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 23 July 2025
mLesInc1.HiC.hap1.20250723.fasta.gz (1.1 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 11 30.67 Mbp 1 0.96 Gbp
20 27 23.31 Mbp 1 0.96 Gbp
30 48 17.74 Mbp 2 0.87 Gbp
40 75 14.52 Mbp 2 0.87 Gbp
50 107 11.94 Mbp 3 0.85 Gbp
60 148 8.79 Mbp 3 0.85 Gbp
70 206 5.99 Mbp 4 0.64 Gbp
80 290 4.21 Mbp 5 380.60 Mbp
90 435 1.99 Mbp 6 372.75 Mbp
100 1268 8.12 Kbp 224 8.12 Kbp
1.000x 1268 4.25 Gbp 224 4.25 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 23 July 2025
mLesInc1.HiC.hap2.20250723.fasta.gz (1.1 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 11 32.94 Mbp 1 1.80 Gbp
20 24 27.29 Mbp 1 1.80 Gbp
30 42 18.64 Mbp 1 1.80 Gbp
40 66 14.93 Mbp 1 1.80 Gbp
50 98 11.20 Mbp 2 0.87 Gbp
60 141 8.33 Mbp 2 0.87 Gbp
70 197 6.44 Mbp 3 0.63 Gbp
80 278 4.03 Mbp 3 0.63 Gbp
90 415 2.07 Mbp 5 371.43 Mbp
100 1104 13.43 Kbp 116 13.43 Kbp
1.000x 1104 4.10 Gbp 116 4.10 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 23 July 2025
mLesInc1.MT.20250723.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mLesInc1.yml (view)
species: Lestoros inca
specimem: mLesInc1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Lestoros_inca/mLesInc1/assembly_vgp_HiC_2.0/mLesInc1.HiC.hap1.20250723.fasta.gz
hap2: s3://genomeark/species/Lestoros_inca/mLesInc1/assembly_vgp_HiC_2.0/mLesInc1.HiC.hap2.20250723.fasta.gz
pretext_hap1: s3://genomeark/species/Lestoros_inca/mLesInc1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mLesInc1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Lestoros_inca/mLesInc1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mLesInc1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Lestoros_inca/mLesInc1/assembly_vgp_HiC_2.0/evaluation/merqury/mLesInc1_png/
pacbio_read_dir: s3://genomeark/species/Lestoros_inca/mLesInc1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Lestoros_inca/mLesInc1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.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 (v0.7) with database PlusPF 2022
  - Pre-curation worklfow (v1.0beta6)
notes: This was a Hifiasm-HiC assembly of mLesInc1 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.