Troglodytes aedon

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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_curated from 23 February 2026
bTroAed1.hap1.cur.20260223.fasta.gz (340.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 78.64 Mbp 1 152.69 Mbp
20 4 46.98 Mbp 2 118.26 Mbp
30 7 36.83 Mbp 3 114.93 Mbp
40 12 22.50 Mbp 5 73.34 Mbp
50 17 18.86 Mbp 6 72.91 Mbp
60 25 13.52 Mbp 8 40.65 Mbp
70 37 7.81 Mbp 12 25.79 Mbp
80 57 5.21 Mbp 18 15.66 Mbp
90 91 2.10 Mbp 30 7.15 Mbp
100 602 4.56 Kbp 343 21.88 Kbp
1.000x 602 1.22 Gbp 343 1.22 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 23 February 2026
bTroAed1.hap2.cur.20260223.fasta.gz (285.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 66.75 Mbp 1 153.84 Mbp
20 4 53.34 Mbp 2 118.56 Mbp
30 6 46.35 Mbp 3 117.83 Mbp
40 9 38.88 Mbp 4 72.70 Mbp
50 13 21.94 Mbp 6 63.88 Mbp
60 19 15.61 Mbp 9 25.78 Mbp
70 29 9.05 Mbp 14 18.67 Mbp
80 46 4.86 Mbp 23 8.46 Mbp
90 78 2.18 Mbp 41 4.73 Mbp
100 498 8.95 Kbp 315 29.56 Kbp
1.000x 498 1.15 Gbp 315 1.15 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.