Turdus migratorius

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bTurMig1 1174.57 Gbp N/A 2.0 TiB
PacBio HiFi (.fq) bTurMig1 54.52 Gbp N/A 42.5 GiB
PacBio HiFi (.bam) bTurMig1 166.32 Gbp N/A 579.3 GiB
Arima bTurMig1 60.52 Gbp N/A 30.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 August 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bTurMig1 PacBio HiFi (subreads) 1174.57 Gbp N/A 2.0 TiB
PacBio HiFi (.fq) 54.52 Gbp N/A 42.5 GiB
PacBio HiFi (.bam) 166.32 Gbp N/A 579.3 GiB
Arima 60.52 Gbp N/A 30.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 August 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 24 July 2025
bTurMig1.hap1.cur.20250724.fasta.gz (323.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 65.20 Mbp 1 158.75 Mbp
20 6 35.35 Mbp 2 119.76 Mbp
30 10 22.86 Mbp 3 119.09 Mbp
40 16 18.41 Mbp 5 75.47 Mbp
50 25 13.64 Mbp 7 68.10 Mbp
60 36 9.86 Mbp 9 40.32 Mbp
70 53 6.12 Mbp 13 22.85 Mbp
80 82 3.60 Mbp 20 15.78 Mbp
90 136 1.47 Mbp 33 7.57 Mbp
100 755 4.57 Kbp 421 15.65 Kbp
1.000x 755 1.30 Gbp 421 1.30 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 22 July 2025
bTurMig1.hap2.cur.20250722.fasta.gz (300.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 37.93 Mbp 1 158.16 Mbp
20 7 26.75 Mbp 2 118.37 Mbp
30 12 23.38 Mbp 3 118.03 Mbp
40 18 19.98 Mbp 5 73.30 Mbp
50 25 16.28 Mbp 7 43.10 Mbp
60 35 10.17 Mbp 10 26.65 Mbp
70 51 5.51 Mbp 16 18.93 Mbp
80 82 2.99 Mbp 26 8.37 Mbp
90 165 0.82 Mbp 53 1.86 Mbp
100 852 191 bp 584 17.46 Kbp
1.000x 852 1.25 Gbp 584 1.25 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/bTurMig1.yml (view)
species: Turdus migratorius
specimen: bTurMig1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Turdus_migratorius/bTurMig1/assembly_vgp_HiC_2.0/bTurMig1.HiC.hap1.20240523.fasta.gz
hap2: s3://genomeark/species/Turdus_migratorius/bTurMig1/assembly_vgp_HiC_2.0/bTurMig1.HiC.hap2.20240523.fasta.gz
pretext_hap1: s3://genomeark/species/Turdus_migratorius/bTurMig1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bTurMig1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Turdus_migratorius/bTurMig1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bTurMig1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Turdus_migratorius/bTurMig1/assembly_vgp_HiC_2.0/evaluation/merqury/bTurMig1_png/
pacbio_read_dir: s3://genomeark/species/Turdus_migratorius/bTurMig1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Turdus_migratorius/bTurMig1/genomic_data/arima/
mito: s3://genomeark/species/Turdus_migratorius/bTurMig1/assembly_MT_rockefeller/bTurMig1.MT.20240524.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy1)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bTurMig1, resulting in two complete haplotypes. 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.