Amblyopsis spelaea

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fAmbSpe1 42.89 Gbp N/A 20.3 GiB
PacBio HiFi (.bam) fAmbSpe1 364.91 Gbp N/A 172.5 GiB
Arima fAmbSpe1 50.82 Gbp N/A 27.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 November 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fAmbSpe1 PacBio HiFi (.fq) 42.89 Gbp N/A 20.3 GiB
PacBio HiFi (.bam) 364.91 Gbp N/A 172.5 GiB
Arima 50.82 Gbp N/A 27.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 7 November 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 14 October 2024
fAmbSpe1.HiC.hap1.20241014.fasta.gz (213.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 12.55 Mbp 2 42.23 Mbp
20 12 9.89 Mbp 4 34.09 Mbp
30 21 7.75 Mbp 7 31.87 Mbp
40 34 5.51 Mbp 9 31.23 Mbp
50 51 4.08 Mbp 12 30.66 Mbp
60 78 2.45 Mbp 15 28.95 Mbp
70 121 1.50 Mbp 18 26.74 Mbp
80 192 0.88 Mbp 21 23.68 Mbp
90 320 418.16 Kbp 27 5.71 Mbp
100 1362 13.96 Kbp 914 13.96 Kbp
1.000x 1362 0.81 Gbp 914 0.81 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 14 October 2024
fAmbSpe1.HiC.hap2.20241014.fasta.gz (224.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 12.03 Mbp 2 45.58 Mbp
20 14 8.92 Mbp 4 36.35 Mbp
30 25 6.68 Mbp 7 34.38 Mbp
40 40 5.26 Mbp 9 34.01 Mbp
50 60 3.82 Mbp 12 30.69 Mbp
60 87 2.48 Mbp 15 28.81 Mbp
70 132 1.46 Mbp 18 26.00 Mbp
80 208 0.89 Mbp 22 21.21 Mbp
90 350 429.13 Kbp 44 1.33 Mbp
100 1155 12.34 Kbp 708 12.34 Kbp
1.000x 1155 0.87 Gbp 708 0.87 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/fAmbSpe1.yaml (view)
species: Amblyopsis spelaea
specimen: fAmbSpe1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Amblyopsis_spelaea/fAmbSpe1/assembly_vgp_HiC_2.0/fAmbSpe1.HiC.hap1.20241014.fasta.gz
hap2: s3://genomeark/species/Amblyopsis_spelaea/fAmbSpe1/assembly_vgp_HiC_2.0/fAmbSpe1.HiC.hap2.20241014.fasta.gz
pretext_hap1: s3://genomeark/species/Amblyopsis_spelaea/fAmbSpe1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fAmbSpe1_hap1__s2.pretext
pretext_hap2: s3://genomeark/species/Amblyopsis_spelaea/fAmbSpe1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fAmbSpe1_hap2__s2.pretext
kmer_spectra_img: s3://genomeark/species/Amblyopsis_spelaea/fAmbSpe1/assembly_vgp_HiC_2.0/evaluation/merqury/fAmbSpe1_png/
pacbio_read_dir: s3://genomeark/species/Amblyopsis_spelaea/fAmbSpe1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Amblyopsis_spelaea/fAmbSpe1/genomic_data/arima/
mito: s3://genomeark/species/Amblyopsis_spelaea/fAmbSpe1/assembly_MT_rockefeller/fAmbSpe1.MT.20241014.fasta.gz.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fAmbSpe1, 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. This is a VGP Phase 1 species we are submitting for dual curation.
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.