Steatornis caripensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bSteCar1 85.93 Gbp N/A 46.7 GiB
PacBio HiFi (.bam) bSteCar1 91.15 Gbp N/A 295.2 GiB
Arima bSteCar1 111.40 Gbp N/A 59.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 October 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bSteCar1 PacBio HiFi (.fq) 85.93 Gbp N/A 46.7 GiB
PacBio HiFi (.bam) 91.15 Gbp N/A 295.2 GiB
Arima 111.40 Gbp N/A 59.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 October 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 17 November 2025
bSteCar1.hap1.cur.20251117.fasta.gz (379.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 220.45 Mbp 1 222.71 Mbp
20 2 128.71 Mbp 2 168.73 Mbp
30 3 83.64 Mbp 3 130.09 Mbp
40 5 71.00 Mbp 4 87.73 Mbp
50 8 44.32 Mbp 5 84.20 Mbp
60 11 32.36 Mbp 8 42.96 Mbp
70 16 22.74 Mbp 12 30.79 Mbp
80 24 14.23 Mbp 17 22.55 Mbp
90 39 5.01 Mbp 24 14.27 Mbp
100 244 52 bp 126 8.31 Kbp
1.000x 244 1.37 Gbp 126 1.37 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 17 November 2025
bSteCar1.hap2.cur.20251117.fasta.gz (310.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 125.76 Mbp 1 223.25 Mbp
20 2 122.02 Mbp 2 169.13 Mbp
30 3 116.74 Mbp 2 169.13 Mbp
40 5 73.19 Mbp 3 130.07 Mbp
50 7 44.91 Mbp 4 83.83 Mbp
60 11 32.31 Mbp 7 43.05 Mbp
70 15 23.99 Mbp 10 26.49 Mbp
80 21 19.02 Mbp 15 21.94 Mbp
90 30 8.42 Mbp 22 14.66 Mbp
100 196 4.71 Kbp 94 9.40 Kbp
1.000x 196 1.20 Gbp 94 1.20 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 October 2025
bSteCar1.MT.20251017.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bSteCar1.yml (view)
species: Steatornis caripensis
specimem: bSteCar1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Steatornis_caripensis/bSteCar1/assembly_vgp_HiC_2.0/bSteCar1.HiC.hap1.20251017.fasta.gz
hap2: s3://genomeark/species/Steatornis_caripensis/bSteCar1/assembly_vgp_HiC_2.0/bSteCar1.HiC.hap2.20251017.fasta.gz
pretext_hap1: s3://genomeark/species/Steatornis_caripensis/bSteCar1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bSteCar1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Steatornis_caripensis/bSteCar1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bSteCar1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Steatornis_caripensis/bSteCar1/assembly_vgp_HiC_2.0/evaluation/merqury/bSteCar1_png/
pacbio_read_dir: s3://genomeark/species/Steatornis_caripensis/bSteCar1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Steatornis_caripensis/bSteCar1/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 (v0.4)
  - VGP8 HiC scaffolding workflow (v3.1) with mapq=10
  - VGP9 decontamination workflow (v1.1)
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bSteCar1 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.