Polymixia lowei

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Resource Primary Assembly Alternate Assembly
GenBank fPolLow1: GCA_040436115.1 fPolLow2: GCA_047511565.1 fPolLow2: GCA_047511595.1 fPolLow1: GCA_040436095.1
ENA fPolLow1: GCA_040436115.1 fPolLow2: GCA_047511565.1 fPolLow2: GCA_047511595.1 fPolLow1: GCA_040436095.1
UCSC Genome Browser fPolLow1: GCA_040436115.1 fPolLow2: GCA_047511565.1 fPolLow2: GCA_047511595.1 fPolLow1: GCA_040436095.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fPolLow2 51.91 Gbp N/A 23.8 GiB
PacBio HiFi (.bam) fPolLow2 51.97 Gbp N/A 169.8 GiB
Arima fPolLow2 58.88 Gbp N/A 31.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 October 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fPolLow2 PacBio HiFi (.fq) 51.91 Gbp N/A 23.8 GiB
PacBio HiFi (.bam) 51.97 Gbp N/A 169.8 GiB
Arima 58.88 Gbp N/A 31.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 October 2024.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 3 December 2024
fPolLow2.hap1.cur.20241203.fasta.gz (171.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 7.93 Mbp 2 33.91 Mbp
20 19 3.92 Mbp 4 31.60 Mbp
30 38 3.27 Mbp 7 29.96 Mbp
40 62 2.24 Mbp 9 29.00 Mbp
50 97 1.68 Mbp 11 28.55 Mbp
60 141 1.34 Mbp 14 28.20 Mbp
70 199 1.04 Mbp 16 27.28 Mbp
80 276 0.73 Mbp 19 23.67 Mbp
90 406 370.66 Kbp 21 22.60 Mbp
100 1078 11.94 Kbp 326 11.94 Kbp
1.000x 1078 0.68 Gbp 326 0.68 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 3 December 2024
fPolLow2.hap2.cur.20241203.fasta.gz (170.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 6.23 Mbp 2 34.27 Mbp
20 22 4.07 Mbp 4 31.76 Mbp
30 41 3.02 Mbp 7 29.70 Mbp
40 66 2.34 Mbp 9 28.83 Mbp
50 98 1.88 Mbp 11 28.70 Mbp
60 138 1.43 Mbp 14 27.89 Mbp
70 193 1.04 Mbp 16 27.29 Mbp
80 273 0.67 Mbp 19 24.13 Mbp
90 408 362.43 Kbp 21 22.30 Mbp
100 955 4.68 Kbp 199 12.06 Kbp
1.000x 955 0.67 Gbp 199 0.67 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 21 October 2024
fPolLow2.MT.20241021.fasta.gz (5.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fPolLow2.yml.yaml (view)
species: Polymixia lowei
specimen: fPolLow2
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Polymixia_lowei/fPolLow2/assembly_vgp_HiC_2.0/fPolLow2.HiC.hap1.20241021.fasta.gz
hap2: s3://genomeark/species/Polymixia_lowei/fPolLow2/assembly_vgp_HiC_2.0/fPolLow2.HiC.hap2.20241021.fasta.gz
pretext_hap1: s3://genomeark/species/Polymixia_lowei/fPolLow2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fPolLow2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Polymixia_lowei/fPolLow2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fPolLow2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Polymixia_lowei/fPolLow2/assembly_vgp_HiC_2.0/evaluation/merqury/fPolLow2_png
pacbio_read_dir: s3://genomeark/species/Polymixia_lowei/fPolLow2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Polymixia_lowei/fPolLow2/genomic_data/arima/
mito: s3://genomeark/species/species/Polymixia_lowei/fPolLow2/assembly_MT_rockefeller/fPolLow2.MT.20241021.fasta.gz.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fPolLow2, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS. The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. This is a VGP Phase 1 species we are submitting for dual curation.
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.