Baeolophus bicolor

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bBaeBic1 1212.48 Gbp N/A 2.1 TiB
PacBio HiFi (.fq) bBaeBic1 52.16 Gbp N/A 44.8 GiB
Arima bBaeBic1 116.95 Gbp N/A 57.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bBaeBic1 PacBio HiFi (subreads) 1212.48 Gbp N/A 2.1 TiB
PacBio HiFi (.fq) 52.16 Gbp N/A 44.8 GiB
Arima 116.95 Gbp N/A 57.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 21 April 2024
bBaeBic1.HiC.hap1.20240421.fasta.gz (297.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 18.10 Mbp 1 152.89 Mbp
20 13 13.45 Mbp 2 122.62 Mbp
30 21 10.85 Mbp 3 116.92 Mbp
40 33 8.84 Mbp 4 75.45 Mbp
50 46 7.32 Mbp 6 64.45 Mbp
60 64 5.52 Mbp 8 37.46 Mbp
70 87 3.96 Mbp 12 23.12 Mbp
80 121 2.55 Mbp 17 19.26 Mbp
90 181 1.29 Mbp 26 7.13 Mbp
100 683 14.76 Kbp 358 14.76 Kbp
1.000x 683 1.09 Gbp 358 1.11 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 21 April 2024
bBaeBic1.HiC.hap2.20240421.fasta.gz (330.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 17.06 Mbp 1 235.74 Mbp
20 14 13.85 Mbp 2 152.80 Mbp
30 25 10.24 Mbp 2 152.80 Mbp
40 38 8.55 Mbp 4 75.47 Mbp
50 54 6.58 Mbp 6 64.47 Mbp
60 75 5.28 Mbp 8 38.26 Mbp
70 101 3.88 Mbp 13 22.41 Mbp
80 142 2.39 Mbp 19 17.24 Mbp
90 213 1.15 Mbp 30 7.33 Mbp
100 679 23.20 Kbp 285 23.20 Kbp
1.000x 679 1.22 Gbp 285 1.24 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 21 April 2024
bBaeBic1.MT.20240421.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bBaeBic1.yml (view)
species: Baeolophus bicolor
specimen: bBaeBic1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Baeolophus_bicolor/bBaeBic1/assembly_vgp_HiC_2.0/bBaeBic1.HiC.hap1.20240421.fasta.gz
hap2: s3://genomeark/species/Baeolophus_bicolor/bBaeBic1/assembly_vgp_HiC_2.0/bBaeBic1.HiC.hap2.20240421.fasta.gz
pretext_hap1: s3://genomeark/species/Baeolophus_bicolor/bBaeBic1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bBaeBic1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Baeolophus_bicolor/bBaeBic1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bBaeBic1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Baeolophus_bicolor/bBaeBic1/assembly_vgp_HiC_2.0/evaluation/merqury/bBaeBic1_png/
pacbio_read_dir: s3://genomeark/species/Baeolophus_bicolor/bBaeBic1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Baeolophus_bicolor/bBaeBic1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Baeolophus_bicolor/bBaeBic1/genomic_data/arima/
mito: s3://genomeark/species/Baeolophus_bicolor/bBaeBic1/assembly_MT_rockefeller/bBaeBic1.MT.20240421.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - solve (3.7)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bBaeBic1, resulting in two complete haplotypes. This sample had Bionano. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT library prep. 
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.