Trichomycterus rosablanca

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Resource Primary Assembly Alternate Assembly
GenBank fTriRos1: GCA_030014385.1 fTriRos1: GCA_030015355.1
ENA fTriRos1: GCA_030014385.1 fTriRos1: GCA_030015355.1
UCSC Genome Browser fTriRos1: GCA_030014385.1 fTriRos1: GCA_030015355.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) fTriRos1 1364.87 Gbp N/A 2.3 TiB
PacBio HiFi (.fq) fTriRos1 46.24 Gbp N/A 29.1 GiB
PacBio HiFi (.bam) fTriRos1 136.75 Gbp N/A 457.0 GiB
Arima fTriRos1 106.56 Gbp N/A 51.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fTriRos1 PacBio HiFi (subreads) 1364.87 Gbp N/A 2.3 TiB
PacBio HiFi (.fq) 46.24 Gbp N/A 29.1 GiB
PacBio HiFi (.bam) 136.75 Gbp N/A 457.0 GiB
Arima 106.56 Gbp N/A 51.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 13 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 25 January 2023
fTriRos1.hap1.cur.20230125.fasta.gz (289.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 35.46 Mbp 1 65.47 Mbp
20 6 27.00 Mbp 2 58.16 Mbp
30 10 22.43 Mbp 4 53.17 Mbp
40 15 15.90 Mbp 7 41.83 Mbp
50 23 13.07 Mbp 9 40.42 Mbp
60 31 10.60 Mbp 12 39.12 Mbp
70 43 7.25 Mbp 15 30.93 Mbp
80 61 5.00 Mbp 18 29.19 Mbp
90 92 1.97 Mbp 22 19.82 Mbp
100 546 1.00 Kbp 348 1.00 Kbp
1.000x 547 1.04 Gbp 349 1.05 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 21 November 2022
fTriRos1.HiC.hap2.20221121.fasta.gz (277.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 26.58 Mbp 1 61.02 Mbp
20 7 17.15 Mbp 2 55.66 Mbp
30 14 13.20 Mbp 4 47.96 Mbp
40 22 10.41 Mbp 7 39.11 Mbp
50 33 8.27 Mbp 9 38.09 Mbp
60 46 6.82 Mbp 12 30.60 Mbp
70 63 5.05 Mbp 16 27.68 Mbp
80 86 3.35 Mbp 20 21.90 Mbp
90 127 1.75 Mbp 25 17.69 Mbp
100 488 1.00 Kbp 296 1.00 Kbp
1.000x 489 0.99 Gbp 297 0.99 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 10 February 2023
fTriRos1.MT.20230210.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fTriRos1.yaml (view)
species: Trichomycterus rosablanca
specimen: fTriRos1
projects: 
  - vgp
hap1: s3://genomeark/species/Trichomycterus_rosablanca/fTriRos1/assembly_vgp_HiC_2.0/fTriRos1.HiC.hap1.20221115.fasta.gz
hap2: s3://genomeark/species/Trichomycterus_rosablanca/fTriRos1/assembly_vgp_HiC_2.0/fTriRos1.HiC.hap2.20221115.fasta.gz
pretext_hap1: s3://genomeark/species/Trichomycterus_rosablanca/fTriRos1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fTriRos1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Trichomycterus_rosablanca/fTriRos1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fTriRos1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Trichomycterus_rosablanca/fTriRos1/assembly_vgp_HiC_2.0/evaluation/fTriRos1_png/
pacbio_read_dir: s3://genomeark/species/Trichomycterus_rosablanca/fTriRos1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Trichomycterus_rosablanca/fTriRos1/genomic_data/arima/
hic_kit: Arima2
pipeline:
  - hifiasm (0.16.1+galaxy4)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of fTriRos1, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with YAHS. The kmer spectra indicates a homogametic specimen. We are submitting hap1 for 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.