Hylocichla mustelina

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bHylMus1 89.86 Gbp N/A 39.4 GiB
PacBio HiFi (.bam) bHylMus1 91.36 Gbp N/A 294.6 GiB
Arima bHylMus1 68.39 Gbp N/A 37.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 December 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bHylMus1 PacBio HiFi (.fq) 89.86 Gbp N/A 39.4 GiB
PacBio HiFi (.bam) 91.36 Gbp N/A 294.6 GiB
Arima 68.39 Gbp N/A 37.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 16 December 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 February 2026
bHylMus1.HiC.hap1.20260206.fasta.gz (326.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 68.59 Mbp 1 165.88 Mbp
20 4 45.32 Mbp 2 120.34 Mbp
30 7 33.32 Mbp 3 118.23 Mbp
40 11 31.19 Mbp 5 75.30 Mbp
50 16 24.56 Mbp 7 49.35 Mbp
60 21 18.52 Mbp 9 36.77 Mbp
70 30 12.03 Mbp 14 22.00 Mbp
80 45 6.47 Mbp 20 16.99 Mbp
90 73 3.13 Mbp 32 7.03 Mbp
100 428 5.15 Kbp 298 5.15 Kbp
1.000x 428 1.24 Gbp 298 1.24 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 February 2026
bHylMus1.HiC.hap2.20260206.fasta.gz (359.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 68.99 Mbp 2 118.66 Mbp
20 4 48.86 Mbp 3 111.50 Mbp
30 8 32.62 Mbp 4 77.64 Mbp
40 12 30.12 Mbp 6 63.64 Mbp
50 18 19.67 Mbp 9 40.69 Mbp
60 26 16.21 Mbp 13 25.85 Mbp
70 35 12.15 Mbp 19 19.67 Mbp
80 52 6.89 Mbp 28 12.78 Mbp
90 85 2.32 Mbp 42 7.36 Mbp
100 519 19.17 Kbp 393 19.17 Kbp
1.000x 519 1.38 Gbp 393 1.38 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 6 February 2026
bHylMus1.MT.20260206.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bHylMus1.yml (view)
species: Hylocichla mustelina
specimem: bHylMus1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Hylocichla_mustelina/bHylMus1/assembly_vgp_HiC_2.0/bHylMus1.HiC.hap1.20260206.fasta.gz
hap2: s3://genomeark/species/Hylocichla_mustelina/bHylMus1/assembly_vgp_HiC_2.0/bHylMus1.HiC.hap2.20260206.fasta.gz
pretext_hap1: s3://genomeark/species/Hylocichla_mustelina/bHylMus1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bHylMus1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Hylocichla_mustelina/bHylMus1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bHylMus1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Hylocichla_mustelina/bHylMus1/assembly_vgp_HiC_2.0/evaluation/merqury/bHylMus1_png/
pacbio_read_dir: s3://genomeark/species/Hylocichla_mustelina/bHylMus1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Hylocichla_mustelina/bHylMus1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.6)
  - VGP4 HiFi HiC assembly workflow (v0.5)
  - VGP8 HiC scaffolding workflow (v3.3) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bHylMus1 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA. The mitoHiFi assembly had 39 annotated genes. Based on the self-alignment, trim the duplicated part (16705bp-18506bp). The final mitogenome assembly is 16797bp. 
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.