Branchiostoma lanceolatum

amphioxus

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  short_name: klBraLanc
  name: Branchiostoma lanceolatum
  taxon_id: 7740
  common_name: amphioxus
  order:
    name: Amphioxiformes
  family:
    name: Branchiostomatidae
  individuals:
    - short_name: klBraLanc2
      biosample_id: SAMEA111562176
      sex:
  genome_size: 577020000
  genome_size_method: GoaT
  project: [ vgp ]
CC BY-SA 3.0 Parent Géry (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) klBraLanc5 50.34 Gbp 87.25x 43.9 GiB
Arima klBraLanc2 104.27 Gbp 180.71x 32.5 GiB
klBraLanc5 48.45 Gbp 83.96x 26.4 GiB
Dovetail Genomics klBraLanc5 82.38 Gbp 142.76x 41.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.58 Gbp.
Last upload on 21 June 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
klBraLanc2 Arima 104.27 Gbp 180.71x 32.5 GiB
klBraLanc5 PacBio HiFi (.fq) 50.34 Gbp 87.25x 43.9 GiB
Arima 48.45 Gbp 83.96x 26.4 GiB
Dovetail Genomics 82.38 Gbp 142.76x 41.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.58 Gbp.
Last upload on 21 June 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 20 June 2023
iBraLan1.hap1.decontam.20230620.fasta.gz (120.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 21.87 Mbp 2 41.10 Mbp
20 6 18.52 Mbp 3 34.41 Mbp
30 9 17.55 Mbp 5 25.68 Mbp
40 13 14.90 Mbp 8 22.94 Mbp
50 17 11.51 Mbp 10 20.72 Mbp
60 23 8.11 Mbp 13 18.34 Mbp
70 32 4.04 Mbp 17 16.41 Mbp
80 0 0
90 0 0
100 0 0
0.795x 141 458.45 Mbp 95 458.45 Mbp
NG based on genome size 0.58 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 20 June 2023
iBraLan1.hap2.decontam.20230620.fasta.gz (120.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 19.17 Mbp 2 43.35 Mbp
20 6 18.15 Mbp 3 40.29 Mbp
30 9 17.38 Mbp 5 32.98 Mbp
40 13 15.69 Mbp 7 23.98 Mbp
50 16 14.72 Mbp 9 22.29 Mbp
60 22 8.15 Mbp 12 19.95 Mbp
70 33 3.43 Mbp 15 17.66 Mbp
80 0 0
90 0 0
100 0 0
0.794x 107 458.35 Mbp 55 458.36 Mbp
NG based on genome size 0.58 Gbp.
Individual 5 Haplotype 1 Assembly
Version assembly_curated from 20 June 2023
klBraLanc5.hap1.cur.20230620.fasta.gz (130.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 21.04 Mbp 2 41.55 Mbp
20 6 18.05 Mbp 3 34.41 Mbp
30 10 14.90 Mbp 5 25.68 Mbp
40 14 12.29 Mbp 8 23.01 Mbp
50 20 8.76 Mbp 10 20.78 Mbp
60 27 6.80 Mbp 13 19.58 Mbp
70 38 3.57 Mbp 16 17.07 Mbp
80 0 0
90 0 0
100 0 0
0.789x 146 455.25 Mbp 65 455.26 Mbp
NG based on genome size 0.58 Gbp.
Individual 5 Haplotype 2 Assembly
Version assembly_curated from 20 June 2023
klBraLanc5.hap2.cur.20230620.fasta.gz (120.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 16.79 Mbp 2 40.41 Mbp
20 7 15.38 Mbp 3 34.45 Mbp
30 11 14.55 Mbp 5 25.72 Mbp
40 16 11.20 Mbp 8 22.63 Mbp
50 22 8.34 Mbp 10 20.57 Mbp
60 30 5.15 Mbp 13 19.39 Mbp
70 44 2.82 Mbp 16 18.55 Mbp
80 0 0
90 0 0
100 0 0
0.794x 137 458.27 Mbp 34 458.29 Mbp
NG based on genome size 0.58 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/klBraLanc5_hap1.yml (view)
species: Branchiostoma lanceolatum
specimen: klBraLanc5
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/assembly_vgp_HiC_2.0/klBraLanc5.HiC.hap1.20230620.fasta.gz
hap2: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/assembly_vgp_HiC_2.0/klBraLanc5.HiC.hap2.20230620.fasta.gz
pretext_hap1: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/klBraLanc5_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/klBraLanc5_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/assembly_vgp_HiC_2.0/evaluation/merqury/klBraLanc5_png/
pacbio_read_dir: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of klBraLanc5, 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. 
assembly_vgp_HiC_2.0/klBraLanc5_hap2.yml (view)
species: Branchiostoma lanceolatum
specimen: klBraLanc5
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/assembly_vgp_HiC_2.0/klBraLanc5.HiC.hap1.20230620.fasta.gz
hap2: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/assembly_vgp_HiC_2.0/klBraLanc5.HiC.hap2.20230620.fasta.gz
pretext_hap1: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/klBraLanc5_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/klBraLanc5_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/assembly_vgp_HiC_2.0/evaluation/merqury/klBraLanc5_png/
pacbio_read_dir: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Branchiostoma_lanceolatum/klBraLanc5/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of klBraLanc5, 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.