Troglodytes aedon

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


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bTroAed1 59.54 Gbp N/A 32.0 GiB
PacBio HiFi (.bam) bTroAed1 59.48 Gbp N/A 236.9 GiB
Arima bTroAed1 107.00 Gbp N/A 55.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 April 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bTroAed1 PacBio HiFi (.fq) 59.54 Gbp N/A 32.0 GiB
PacBio HiFi (.bam) 59.48 Gbp N/A 236.9 GiB
Arima 107.00 Gbp N/A 55.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 23 April 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 June 2024
bTroAed1.HiC.hap1.20240606.fasta.gz (325.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 58.07 Mbp 1 151.81 Mbp
20 4 46.68 Mbp 2 118.26 Mbp
30 7 41.16 Mbp 3 114.65 Mbp
40 10 30.99 Mbp 4 102.07 Mbp
50 15 21.94 Mbp 6 72.02 Mbp
60 21 15.17 Mbp 8 40.37 Mbp
70 31 9.38 Mbp 11 22.11 Mbp
80 47 5.57 Mbp 17 15.61 Mbp
90 78 2.28 Mbp 29 6.30 Mbp
100 538 21.88 Kbp 355 21.88 Kbp
1.000x 538 1.17 Gbp 355 1.17 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 June 2024
bTroAed1.HiC.hap2.20240606.fasta.gz (327.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 78.72 Mbp 1 152.76 Mbp
20 4 57.04 Mbp 2 117.83 Mbp
30 6 39.12 Mbp 3 107.11 Mbp
40 10 25.25 Mbp 5 72.70 Mbp
50 15 18.67 Mbp 7 40.40 Mbp
60 22 12.92 Mbp 11 22.13 Mbp
70 35 7.05 Mbp 17 15.66 Mbp
80 55 4.73 Mbp 28 7.79 Mbp
90 92 2.08 Mbp 49 4.24 Mbp
100 550 20.87 Kbp 338 22.67 Kbp
1.000x 550 1.21 Gbp 338 1.21 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 June 2024
bTroAed1.MT.20240606.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bTroAed1.yml (view)
species: Troglodytes aedon
specimen: bTroAed1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Troglodytes_aedon/bTroAed1/assembly_vgp_HiC_2.0/bTroAed1.HiC.hap1.20240606.fasta.gz
hap2: s3://genomeark/species/Troglodytes_aedon/bTroAed1/assembly_vgp_HiC_2.0/bTroAed1.HiC.hap2.20240606.fasta.gz
pretext_hap1: s3://genomeark/species/Troglodytes_aedon/bTroAed1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bTroAed1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Troglodytes_aedon/bTroAed1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bTroAed1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Troglodytes_aedon/bTroAed1/assembly_vgp_HiC_2.0/evaluation/merqury/bTroAed1_png/
pacbio_read_dir: s3://genomeark/species/Troglodytes_aedon/bTroAed1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Troglodytes_aedon/bTroAed1/genomic_data/arima/
mito: s3://genomeark/species/Troglodytes_aedon/bTroAed1/assembly_MT_rockefeller/bTroAed1.MT.20240606.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy1)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bTroAed1, resulting in two complete haplotypes. This sample did not have Bionano data. Both haplotypes underwent purge_dups with REPEATS kept in. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT. The assembly was performed on usegalaxy MAIN server (vgp.usegalaxy.org).
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.