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
Arima bTurMig1 60.52 Gbp N/A 30.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2024.
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
Arima 60.52 Gbp N/A 30.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 23 May 2024
bTurMig1.HiC.hap1.20240523.fasta.gz (314.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 65.20 Mbp 1 158.98 Mbp
20 4 46.96 Mbp 2 119.09 Mbp
30 7 35.35 Mbp 3 113.65 Mbp
40 12 21.47 Mbp 4 74.47 Mbp
50 17 18.41 Mbp 6 64.01 Mbp
60 25 12.34 Mbp 9 38.11 Mbp
70 37 6.78 Mbp 13 20.91 Mbp
80 60 3.62 Mbp 20 12.30 Mbp
90 107 1.49 Mbp 35 3.65 Mbp
100 627 15.65 Kbp 445 15.65 Kbp
1.000x 627 1.15 Gbp 445 1.15 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 23 May 2024
bTurMig1.HiC.hap2.20240523.fasta.gz (372.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 29.83 Mbp 1 157.81 Mbp
20 10 23.95 Mbp 3 112.98 Mbp
30 16 20.80 Mbp 4 92.04 Mbp
40 23 17.08 Mbp 6 73.30 Mbp
50 33 11.77 Mbp 8 43.10 Mbp
60 46 9.03 Mbp 12 21.98 Mbp
70 68 5.20 Mbp 19 15.65 Mbp
80 104 3.05 Mbp 32 7.67 Mbp
90 193 0.85 Mbp 68 1.89 Mbp
100 959 17.46 Kbp 625 17.46 Kbp
1.000x 959 1.40 Gbp 625 1.40 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.