Struthio camelus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bStrCam1 117.52 Gbp N/A 61.9 GiB
PacBio HiFi (.bam) bStrCam1 119.33 Gbp N/A 491.5 GiB
Arima bStrCam1 413.26 Gbp N/A 207.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 April 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bStrCam1 PacBio HiFi (.fq) 117.52 Gbp N/A 61.9 GiB
PacBio HiFi (.bam) 119.33 Gbp N/A 491.5 GiB
Arima 413.26 Gbp N/A 207.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 April 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 15 June 2024
bStrCam1.hap1.cur.20240615.fasta.gz (402.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 84.05 Mbp 1 225.57 Mbp
20 4 61.97 Mbp 2 173.67 Mbp
30 6 54.04 Mbp 3 148.28 Mbp
40 10 35.43 Mbp 4 89.93 Mbp
50 14 28.83 Mbp 6 84.63 Mbp
60 20 22.60 Mbp 7 70.39 Mbp
70 27 15.30 Mbp 11 34.55 Mbp
80 41 9.25 Mbp 16 25.22 Mbp
90 62 4.72 Mbp 23 14.16 Mbp
100 410 12.52 Kbp 294 12.52 Kbp
1.000x 410 1.45 Gbp 294 1.45 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 15 June 2024
bStrCam1.hap2.cur.20240615.fasta.gz (373.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 83.22 Mbp 1 224.66 Mbp
20 4 60.65 Mbp 2 171.62 Mbp
30 7 36.77 Mbp 3 145.08 Mbp
40 11 31.45 Mbp 4 86.63 Mbp
50 15 28.54 Mbp 5 74.71 Mbp
60 21 22.48 Mbp 8 39.89 Mbp
70 28 15.51 Mbp 13 28.69 Mbp
80 41 8.28 Mbp 18 21.32 Mbp
90 64 3.89 Mbp 29 7.84 Mbp
100 340 17.94 Kbp 258 17.94 Kbp
1.000x 340 1.38 Gbp 258 1.38 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 28 March 2024
bStrCam1.MT.20240328.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bStrCam1.yml (view)
species: Struthio camelus
specimen: bStrCam1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Struthio_camelus/bStrCam1/assembly_vgp_HiC_2.0/bStrCam1.HiC.hap1.20240327.fasta.gz
hap2: s3://genomeark/species/Struthio_camelus/bStrCam1/assembly_vgp_HiC_2.0/bStrCam1.HiC.hap2.20240327.fasta.gz
pretext_hap1: s3://genomeark/species/Struthio_camelus/bStrCam1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bStrCam1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Struthio_camelus/bStrCam1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bStrCam1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Struthio_camelus/bStrCam1/assembly_vgp_HiC_2.0/evaluation/merqury/bStrCam1_png/
pacbio_read_dir: s3://genomeark/species/Struthio_camelus/bStrCam1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Struthio_camelus/bStrCam1/genomic_data/arima/
mito: s3://genomeark/species/Struthio_camelus/bStrCam1/assembly_MT_rockefeller/bStrCam1.MT.20240328.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bStrCam1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. 
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.