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_vgp_HiC_2.0 from 14 December 2022
iBraLan1.HiC.hap1.20221214.fasta.gz (135.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 24.03 Mbp 0 59.25 Mbp
20 4 19.14 Mbp 1 40.22 Mbp
30 6 18.14 Mbp 3 32.88 Mbp
40 9 17.99 Mbp 4 25.60 Mbp
50 12 16.38 Mbp 6 23.14 Mbp
60 15 14.88 Mbp 8 22.28 Mbp
70 18 12.89 Mbp 11 19.57 Mbp
80 23 7.47 Mbp 13 18.94 Mbp
90 33 3.09 Mbp 16 16.72 Mbp
100 177 17.02 Kbp 131 17.02 Kbp
1.000x 178 473.21 Mbp 132 473.22 Mbp
NG based on genome size 0.58 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 14 December 2022
iBraLan1.HiC.hap2.20221214.fasta.gz (126.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 23.51 Mbp 1 43.29 Mbp
20 3 19.00 Mbp 2 40.91 Mbp
30 6 18.05 Mbp 3 34.18 Mbp
40 8 17.06 Mbp 4 31.54 Mbp
50 11 15.10 Mbp 6 24.09 Mbp
60 14 11.17 Mbp 7 22.27 Mbp
70 19 8.58 Mbp 10 20.35 Mbp
80 26 5.52 Mbp 12 19.69 Mbp
90 37 2.12 Mbp 14 17.96 Mbp
100 103 21.93 Kbp 46 21.93 Kbp
1.000x 104 442.08 Mbp 47 442.09 Mbp
NG based on genome size 0.58 Gbp.
Individual 2 Haplotype 1 Assembly
Version assembly_cambridge from 11 April 2024
klBraLanc2.hap1.asm.20240411.fasta.gz (134.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 7.89 Mbp 2 40.94 Mbp
20 15 6.26 Mbp 3 34.91 Mbp
30 26 4.21 Mbp 5 27.24 Mbp
40 41 3.35 Mbp 8 24.11 Mbp
50 61 2.66 Mbp 10 21.45 Mbp
60 84 2.24 Mbp 13 20.16 Mbp
70 116 1.46 Mbp 16 17.47 Mbp
80 193 225.66 Kbp 19 15.67 Mbp
90 0 0
100 0 0
0.815x 351 470.29 Mbp 160 470.33 Mbp
NG based on genome size 0.58 Gbp.
Individual 2 Haplotype 2 Assembly
Version assembly_cambridge from 11 April 2024
klBraLanc2.hap2.asm.20240411.fasta.gz (132.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 6.83 Mbp 2 40.96 Mbp
20 17 5.24 Mbp 3 33.84 Mbp
30 30 4.40 Mbp 5 27.13 Mbp
40 44 3.63 Mbp 8 23.57 Mbp
50 62 2.92 Mbp 10 20.70 Mbp
60 84 2.25 Mbp 13 19.87 Mbp
70 118 1.25 Mbp 16 18.17 Mbp
80 209 96.03 Kbp 23 144.64 Kbp
90 0 0
100 0 0
0.804x 269 464.09 Mbp 81 464.13 Mbp
NG based on genome size 0.58 Gbp.
Individual 2 Mitochondrial Assembly
Version assembly_MT_cambridge from 11 April 2024
klBraLanc2.MT.20240411.fasta.gz (4.9 KiB)

Quality: not computed
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.