Psaltriparus minimus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bPsaMin1 57.54 Gbp N/A 25.5 GiB
PacBio HiFi (.bam) bPsaMin1 58.30 Gbp N/A 190.2 GiB
Arima bPsaMin1 128.49 Gbp N/A 66.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 31 October 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bPsaMin1 PacBio HiFi (.fq) 57.54 Gbp N/A 25.5 GiB
PacBio HiFi (.bam) 58.30 Gbp N/A 190.2 GiB
Arima 128.49 Gbp N/A 66.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 31 October 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 10 November 2025
bPsaMin1.HiC.hap1.20251110.fasta.gz (303.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 63.28 Mbp 1 154.87 Mbp
20 4 60.71 Mbp 2 121.11 Mbp
30 7 32.17 Mbp 3 116.83 Mbp
40 11 23.72 Mbp 4 94.84 Mbp
50 16 19.56 Mbp 6 75.76 Mbp
60 22 17.02 Mbp 7 63.14 Mbp
70 30 13.07 Mbp 10 32.17 Mbp
80 40 8.41 Mbp 15 22.62 Mbp
90 63 3.60 Mbp 23 9.86 Mbp
100 454 10.13 Kbp 240 10.13 Kbp
1.000x 454 1.16 Gbp 240 1.16 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 10 November 2025
bPsaMin1.HiC.hap2.20251110.fasta.gz (305.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 55.95 Mbp 1 158.47 Mbp
20 5 33.98 Mbp 2 120.42 Mbp
30 9 29.69 Mbp 3 114.06 Mbp
40 14 22.28 Mbp 4 93.54 Mbp
50 19 18.58 Mbp 6 72.16 Mbp
60 26 16.57 Mbp 8 42.38 Mbp
70 35 11.89 Mbp 11 27.59 Mbp
80 47 6.31 Mbp 16 21.00 Mbp
90 77 2.02 Mbp 25 9.37 Mbp
100 478 16.16 Kbp 288 16.16 Kbp
1.000x 478 1.18 Gbp 288 1.18 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 November 2025
bPsaMin1.MT.20251110.fasta.gz (5.5 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bPsaMin1.yml (view)
species: Psaltriparus minimus
specimem: bPsaMin1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Psaltriparus_minimus/bPsaMin1/assembly_vgp_HiC_2.0/bPsaMin1.HiC.hap1.20251110.fasta.gz
hap2: s3://genomeark/species/Psaltriparus_minimus/bPsaMin1/assembly_vgp_HiC_2.0/bPsaMin1.HiC.hap2.20251110.fasta.gz
pretext_hap1: s3://genomeark/species/Psaltriparus_minimus/bPsaMin1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bPsaMin1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Psaltriparus_minimus/bPsaMin1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bPsaMin1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Psaltriparus_minimus/bPsaMin1/assembly_vgp_HiC_2.0/evaluation/merqury/bPsaMin1_png/
pacbio_read_dir: s3://genomeark/species/Psaltriparus_minimus/bPsaMin1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Psaltriparus_minimus/bPsaMin1/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 (v0.4)
  - VGP8 HiC scaffolding workflow (v3.1) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bPsaMin1 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.