Parvimolge townsendi

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aParTow1 660.29 Gbp N/A 317.6 GiB
PacBio HiFi (.bam) aParTow1 689.18 Gbp N/A 2.3 TiB
Arima aParTow1 1493.78 Gbp N/A 796.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 October 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aParTow1 PacBio HiFi (.fq) 660.29 Gbp N/A 317.6 GiB
PacBio HiFi (.bam) 689.18 Gbp N/A 2.3 TiB
Arima 1493.78 Gbp N/A 796.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 2 October 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 June 2026
aParTow1.HiC.hap1.20260606.fasta.gz (6.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 45 44.39 Mbp 1 3.94 Gbp
20 112 32.76 Mbp 2 3.04 Gbp
30 199 25.87 Mbp 3 2.12 Gbp
40 310 20.55 Mbp 4 2.08 Gbp
50 447 16.37 Mbp 5 2.07 Gbp
60 617 13.15 Mbp 6 1.92 Gbp
70 835 10.07 Mbp 8 1.40 Gbp
80 1143 6.83 Mbp 10 1.32 Gbp
90 1651 3.37 Mbp 12 1.08 Gbp
100 8357 5.98 Kbp 5397 5.98 Kbp
1.000x 8357 25.19 Gbp 5397 25.19 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 June 2026
aParTow1.HiC.hap2.20260606.fasta.gz (6.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 48 42.19 Mbp 1 4.14 Gbp
20 118 31.51 Mbp 2 3.78 Gbp
30 205 26.21 Mbp 2 3.78 Gbp
40 312 21.02 Mbp 4 1.84 Gbp
50 441 17.75 Mbp 5 1.48 Gbp
60 598 14.17 Mbp 7 1.18 Gbp
70 801 10.60 Mbp 9 1.07 Gbp
80 1083 7.31 Mbp 12 0.75 Gbp
90 1549 3.66 Mbp 16 409.60 Mbp
100 6170 5.19 Kbp 3286 5.19 Kbp
1.000x 6170 24.89 Gbp 3286 24.89 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/aParTow1.yml (view)
species: Parvimolge townsendi
specimen: aParTow1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Parvimolge_townsendi/aParTow1/assembly_vgp_HiC_2.0/aParTow1.HiC.hap1.20260606.fasta.gz
hap2: s3://genomeark/species/Parvimolge_townsendi/aParTow1/assembly_vgp_HiC_2.0/aParTow1.HiC.hap2.20260606.fasta.gz
pretext_hap1: s3://genomeark/species/Parvimolge_townsendi/aParTow1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/aParTow1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Parvimolge_townsendi/aParTow1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/aParTow1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Parvimolge_townsendi/aParTow1/assembly_vgp_HiC_2.0/evaluation/merqury/aParTow1_png/
pacbio_read_dir: s3://genomeark/species/Parvimolge_townsendi/aParTow1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Parvimolge_townsendi/aParTow1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10. Note that the YaHS scaffolding completed, but the following QC steps failed because the size of the largest few scaffolds is >2.1Gb.
  - VGP9 decontamination workflow (v1.3). Note that the largest 3 scaffolds (>2.1Gb) were split into smaller parts.
  - Pre-curation workflow (v20260526 update) with mapq=10, keep HiC duplicates and generate ultra-high resolution map
notes: This was a Hifiasm-HiC assembly of aParTow1 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. No HiFi reads were mapped to the mitogenome reference. Hence no mitogenome was assembled.
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.