Tapirus indicus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mTapInd1 2090.76 Gbp N/A 3.6 TiB
PacBio HiFi (.fq) mTapInd1 93.39 Gbp N/A 69.2 GiB
PacBio HiFi (.bam) mTapInd1 300.36 Gbp N/A 1.0 TiB
Dovetail Genomics mTapInd1 143.32 Gbp N/A 79.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mTapInd1 PacBio HiFi (subreads) 2090.76 Gbp N/A 3.6 TiB
PacBio HiFi (.fq) 93.39 Gbp N/A 69.2 GiB
PacBio HiFi (.bam) 300.36 Gbp N/A 1.0 TiB
Dovetail Genomics 143.32 Gbp N/A 79.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 21 July 2023
mTapInd1.hap1.cur.20230721.fasta.gz (720.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 141.90 Mbp 2 156.08 Mbp
20 5 87.75 Mbp 4 154.87 Mbp
30 8 70.66 Mbp 5 147.66 Mbp
40 12 61.97 Mbp 7 137.89 Mbp
50 16 52.01 Mbp 9 129.32 Mbp
60 21 43.62 Mbp 11 115.44 Mbp
70 27 38.01 Mbp 13 94.77 Mbp
80 35 29.19 Mbp 16 61.97 Mbp
90 47 14.18 Mbp 21 42.04 Mbp
100 338 14.56 Kbp 259 14.56 Kbp
1.000x 338 2.50 Gbp 259 2.50 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 21 July 2023
mTapInd1.hap2.cur.20230721.fasta.gz (716.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 140.96 Mbp 2 155.12 Mbp
20 5 90.55 Mbp 4 151.14 Mbp
30 7 78.62 Mbp 5 146.28 Mbp
40 11 62.71 Mbp 7 137.13 Mbp
50 15 56.55 Mbp 9 129.75 Mbp
60 21 42.12 Mbp 11 114.52 Mbp
70 27 35.50 Mbp 13 92.47 Mbp
80 35 25.52 Mbp 16 61.86 Mbp
90 48 10.86 Mbp 21 42.19 Mbp
100 284 24.50 Kbp 192 24.50 Kbp
1.000x 284 2.48 Gbp 192 2.48 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 12 May 2023
mTapInd1.MT.20230512.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mTapInd1_hap1.yml (view)
species: Tapirus indicus
specimen: mTapInd1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_vgp_HiC_2.0/mTapInd1.HiC.hap1.20230427.fasta.gz
hap2: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_vgp_HiC_2.0/mTapInd1.HiC.hap2.20230427.fasta.gz
pretext_hap1: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mTapInd1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mTapInd1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_vgp_HiC_2.0/evaluation/merqury/mTapInd1_png/
mito: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_MT_rockefeller/mTapInd1.MT.20230512.fasta.gz
mito_gb: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_MT_rockefeller/mTapInd1.MT.20230512.gb
pacbio_read_dir: s3://genomeark/species/Tapirus_indicus/mTapInd1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Tapirus_indicus/mTapInd1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of mTapInd1, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. TThe kmer spectra indicate a homogametic specimen. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap1. 
assembly_vgp_HiC_2.0/mTapInd1_hap2.yml (view)
species: Tapirus indicus
specimen: mTapInd1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_vgp_HiC_2.0/mTapInd1.HiC.hap1.20230427.fasta.gz
hap2: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_vgp_HiC_2.0/mTapInd1.HiC.hap2.20230427.fasta.gz
pretext_hap1: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mTapInd1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mTapInd1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_vgp_HiC_2.0/evaluation/merqury/mTapInd1_png/
mito: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_MT_rockefeller/mTapInd1.MT.20230512.fasta.gz
mito_gb: s3://genomeark/species/Tapirus_indicus/mTapInd1/assembly_MT_rockefeller/mTapInd1.MT.20230512.gb
pacbio_read_dir: s3://genomeark/species/Tapirus_indicus/mTapInd1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Tapirus_indicus/mTapInd1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of mTapInd1, resulting in two complete haplotypes. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. TThe kmer spectra indicate a homogametic specimen. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap2. 
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.