Thalassoma bifasciatum

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


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fThaBif1 57.47 Gbp N/A 27.5 GiB
PacBio HiFi (.bam) fThaBif1 57.47 Gbp N/A 232.5 GiB
Arima fThaBif1 89.41 Gbp N/A 47.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fThaBif1 PacBio HiFi (.fq) 57.47 Gbp N/A 27.5 GiB
PacBio HiFi (.bam) 57.47 Gbp N/A 232.5 GiB
Arima 89.41 Gbp N/A 47.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 24 June 2024
fThaBif1.HiC.hap1.20240624.fasta.gz (217.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 34.51 Mbp 2 38.83 Mbp
20 5 33.71 Mbp 5 36.87 Mbp
30 7 28.55 Mbp 7 35.38 Mbp
40 10 27.68 Mbp 9 34.69 Mbp
50 13 23.43 Mbp 11 34.60 Mbp
60 17 18.85 Mbp 13 33.71 Mbp
70 21 16.41 Mbp 16 31.01 Mbp
80 27 13.31 Mbp 18 30.63 Mbp
90 34 8.32 Mbp 21 26.75 Mbp
100 163 11.36 Kbp 90 11.36 Kbp
1.000x 163 0.78 Gbp 90 0.78 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 24 June 2024
fThaBif1.HiC.hap2.20240624.fasta.gz (217.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 34.83 Mbp 2 38.79 Mbp
20 5 30.00 Mbp 5 36.52 Mbp
30 8 27.28 Mbp 7 35.61 Mbp
40 11 26.05 Mbp 9 34.83 Mbp
50 14 23.04 Mbp 11 34.40 Mbp
60 18 16.47 Mbp 13 34.04 Mbp
70 23 14.25 Mbp 16 31.59 Mbp
80 29 12.04 Mbp 18 30.81 Mbp
90 37 6.78 Mbp 21 26.22 Mbp
100 155 10.85 Kbp 81 10.85 Kbp
1.000x 155 0.78 Gbp 81 0.78 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/fThaBif1.yml (view)
species: Thalassoma bifasciatum
specimen: fThaBif1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Thalassoma_bifasciatum/fThaBif1/assembly_vgp_HiC_2.0/fThaBif1.HiC.hap1.20240624.fasta.gz
hap2: s3://genomeark/species/Thalassoma_bifasciatum/fThaBif1/assembly_vgp_HiC_2.0/fThaBif1.HiC.hap2.20240624.fasta.gz
pretext_hap1: s3://genomeark/species/Thalassoma_bifasciatum/fThaBif1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fThaBif1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Thalassoma_bifasciatum/fThaBif1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fThaBif1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Thalassoma_bifasciatum/fThaBif1/assembly_vgp_HiC_2.0/evaluation/merqury/hap1_purged/fThaBif1_png/
pacbio_read_dir: s3://genomeark/species/Thalassoma_bifasciatum/fThaBif1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Thalassoma_bifasciatum/fThaBif1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy1)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fThaBif1, resulting in two complete haplotypes. Each haplotype underwent purging (while keeping repeats), and then the scaffolding consisted of YaHS.  The HiC prep kit used was Arima, so the HiC reads require trimming 5 bp off the 5' end. The assembly was performed on the Rockefeller University VGL instance. 
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.