Thryothorus ludovicianus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bThrLud1 42.92 Gbp N/A 21.0 GiB
PacBio HiFi (.bam) bThrLud1 43.78 Gbp N/A 145.0 GiB
Arima bThrLud1 88.63 Gbp N/A 46.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bThrLud1 PacBio HiFi (.fq) 42.92 Gbp N/A 21.0 GiB
PacBio HiFi (.bam) 43.78 Gbp N/A 145.0 GiB
Arima 88.63 Gbp N/A 46.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 September 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 25 September 2025
bThrLud1.HiC.hap1.20250925.fasta.gz (290.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 29.80 Mbp 1 152.00 Mbp
20 9 21.23 Mbp 2 116.77 Mbp
30 14 18.68 Mbp 3 114.59 Mbp
40 21 15.23 Mbp 4 93.04 Mbp
50 31 10.35 Mbp 6 69.22 Mbp
60 44 7.33 Mbp 8 41.04 Mbp
70 63 5.01 Mbp 12 24.00 Mbp
80 96 2.65 Mbp 17 17.32 Mbp
90 168 0.89 Mbp 27 7.06 Mbp
100 965 9.28 Kbp 471 9.28 Kbp
1.000x 965 1.17 Gbp 471 1.17 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 25 September 2025
bThrLud1.HiC.hap2.20250925.fasta.gz (289.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 27.75 Mbp 1 151.10 Mbp
20 9 22.20 Mbp 2 116.08 Mbp
30 14 18.36 Mbp 3 114.73 Mbp
40 21 15.66 Mbp 4 96.05 Mbp
50 29 12.94 Mbp 6 69.81 Mbp
60 40 8.85 Mbp 7 63.18 Mbp
70 57 5.44 Mbp 10 35.72 Mbp
80 83 3.41 Mbp 15 19.78 Mbp
90 134 1.45 Mbp 23 10.78 Mbp
100 582 16.78 Kbp 214 16.78 Kbp
1.000x 582 1.13 Gbp 214 1.13 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 25 September 2025
bThrLud1.MT.20250925.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bThrLud1.yml (view)
species: Thryothorus ludovicianus
specimem: bThrLud1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Thryothorus_ludovicianus/bThrLud1/assembly_vgp_HiC_2.0/bThrLud1.HiC.hap1.20250925.fasta.gz
hap2: s3://genomeark/species/Thryothorus_ludovicianus/bThrLud1/assembly_vgp_HiC_2.0/bThrLud1.HiC.hap2.20250925.fasta.gz
pretext_hap1: s3://genomeark/species/Thryothorus_ludovicianus/bThrLud1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bThrLud1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Thryothorus_ludovicianus/bThrLud1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bThrLud1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Thryothorus_ludovicianus/bThrLud1/assembly_vgp_HiC_2.0/evaluation/merqury/bThrLud1_png/
pacbio_read_dir: s3://genomeark/species/Thryothorus_ludovicianus/bThrLud1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Thryothorus_ludovicianus/bThrLud1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy2)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v2.2) with mapq=10
  - VGP9 decontamination workflow unpublished using FCS (0.5.5+galaxy0) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bThrLud1 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.
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.