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_curated from 5 December 2024
fAmbSpe1.hap1.cur.20241205.fasta.gz (214.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 12.29 Mbp 3 37.11 Mbp
20 12 9.89 Mbp 5 35.05 Mbp
30 21 8.07 Mbp 7 34.21 Mbp
40 34 5.56 Mbp 10 34.06 Mbp
50 51 4.01 Mbp 12 32.24 Mbp
60 78 2.45 Mbp 15 31.64 Mbp
70 121 1.51 Mbp 17 31.48 Mbp
80 191 0.91 Mbp 20 28.95 Mbp
90 318 429.20 Kbp 23 25.89 Mbp
100 1357 13.96 Kbp 891 13.96 Kbp
1.000x 1357 0.82 Gbp 891 0.82 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 5 December 2024
fAmbSpe1.hap2.cur.20241205.fasta.gz (223.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 11.64 Mbp 3 37.04 Mbp
20 15 8.69 Mbp 5 36.37 Mbp
30 26 6.53 Mbp 7 36.35 Mbp
40 42 5.00 Mbp 10 34.38 Mbp
50 62 3.81 Mbp 12 32.39 Mbp
60 91 2.43 Mbp 15 31.66 Mbp
70 137 1.42 Mbp 18 31.12 Mbp
80 214 0.87 Mbp 21 29.26 Mbp
90 356 421.43 Kbp 27 1.66 Mbp
100 1151 12.34 Kbp 667 12.34 Kbp
1.000x 1151 0.86 Gbp 667 0.87 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 14 October 2024
fAmbSpe1.MT.20241014.fasta.gz (5.7 KiB)

Quality: not computed
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.