Aegotheles albertisi

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bAegAlb1 50.42 Gbp N/A 22.2 GiB
PacBio HiFi (.bam) bAegAlb1 455.75 Gbp N/A 200.6 GiB
Arima bAegAlb1 122.04 Gbp N/A 64.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 25 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bAegAlb1 PacBio HiFi (.fq) 50.42 Gbp N/A 22.2 GiB
PacBio HiFi (.bam) 455.75 Gbp N/A 200.6 GiB
Arima 122.04 Gbp N/A 64.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 25 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 20 November 2023
bAegAlb1.HiC.hap1.20231120.fasta.gz (336.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 17.49 Mbp 2 84.73 Mbp
20 13 15.91 Mbp 3 82.25 Mbp
30 21 14.23 Mbp 4 81.79 Mbp
40 30 11.70 Mbp 6 59.52 Mbp
50 40 10.22 Mbp 8 46.90 Mbp
60 55 6.07 Mbp 11 41.67 Mbp
70 76 4.76 Mbp 14 27.45 Mbp
80 105 3.12 Mbp 19 19.68 Mbp
90 164 1.23 Mbp 26 12.23 Mbp
100 1013 3.44 Kbp 608 3.44 Kbp
1.000x 1013 1.16 Gbp 608 1.16 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 20 November 2023
bAegAlb1.HiC.hap2.20231120.fasta.gz (307.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 21.94 Mbp 1 110.21 Mbp
20 10 17.34 Mbp 3 81.88 Mbp
30 17 14.86 Mbp 4 80.94 Mbp
40 25 12.56 Mbp 6 57.10 Mbp
50 34 9.60 Mbp 8 46.61 Mbp
60 47 7.03 Mbp 10 42.05 Mbp
70 64 5.24 Mbp 13 27.36 Mbp
80 87 3.94 Mbp 18 20.68 Mbp
90 132 1.39 Mbp 24 12.81 Mbp
100 887 4.48 Kbp 538 4.48 Kbp
1.000x 887 1.06 Gbp 538 1.06 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 5 January 2024
bAegAlb1.MT.20240105.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bAegAlb1_hap1.yml (view)
species: Aegotheles albertisi
specimen: bAegAlb1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_vgp_HiC_2.0/bAegAlb1.HiC.hap1.20231120.fasta.gz
hap2: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_vgp_HiC_2.0/bAegAlb1.HiC.hap2.20231120.fasta.gz
pretext_hap1: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bAegAlb1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bAegAlb1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_vgp_HiC_2.0/evaluation/merqury/bAegAlb1_png/
pacbio_read_dir: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/genomic_data/arima/
mito: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_MT_rockefeller/bAegAlb1.MT.20230105.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
  - mitohifi (3+galaxy0)
notes: This was a Hifiasm-HiC assembly of bAegAlb1, resulting in two complete haplotypes. These assemblies underwent purge_dups. 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/bAegAlb1_hap2.yml (view)
species: Aegotheles albertisi
specimen: bAegAlb1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_vgp_HiC_2.0/bAegAlb1.HiC.hap1.20231120.fasta.gz
hap2: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_vgp_HiC_2.0/bAegAlb1.HiC.hap2.20231120.fasta.gz
pretext_hap1: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bAegAlb1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bAegAlb1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_vgp_HiC_2.0/evaluation/merqury/bAegAlb1_png/
pacbio_read_dir: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/genomic_data/arima/
mito: s3://genomeark/species/Aegotheles_albertisi/bAegAlb1/assembly_MT_rockefeller/bAegAlb1.MT.20230105.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
  - mitohifi (3+galaxy0)
notes: This was a Hifiasm-HiC assembly of bAegAlb1, resulting in two complete haplotypes. These assemblies underwent purge_dups. 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.