Inia geoffrensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mIniGeo1 100.52 Gbp N/A 123.1 GiB
Dovetail Genomics mIniGeo1 148.27 Gbp N/A 78.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mIniGeo1 PacBio HiFi (.fq) 100.52 Gbp N/A 123.1 GiB
Dovetail Genomics 148.27 Gbp N/A 78.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 7 January 2024
mIniGeo1.hap1.cur.20240107.fasta.gz (671.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 101.36 Mbp 2 188.53 Mbp
20 6 91.40 Mbp 3 185.96 Mbp
30 9 68.54 Mbp 5 152.62 Mbp
40 14 46.02 Mbp 7 134.57 Mbp
50 20 40.89 Mbp 9 117.43 Mbp
60 28 31.47 Mbp 12 106.87 Mbp
70 38 22.21 Mbp 14 100.65 Mbp
80 53 14.65 Mbp 17 88.88 Mbp
90 104 1.69 Mbp 21 63.99 Mbp
100 1186 3.06 Kbp 902 3.06 Kbp
1.000x 1186 2.75 Gbp 902 2.75 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 12 December 2023
mIniGeo1.hap2.cur.20231212.fasta.gz (692.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 124.46 Mbp 2 187.29 Mbp
20 5 96.08 Mbp 3 185.87 Mbp
30 8 67.77 Mbp 5 154.65 Mbp
40 13 47.05 Mbp 7 120.47 Mbp
50 19 41.94 Mbp 9 109.67 Mbp
60 25 35.33 Mbp 11 105.89 Mbp
70 34 21.04 Mbp 14 91.96 Mbp
80 48 15.58 Mbp 16 88.72 Mbp
90 90 1.83 Mbp 20 63.78 Mbp
100 1040 1.00 Kbp 800 1.00 Kbp
1.000x 1040 2.54 Gbp 800 2.54 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 23 May 2023
mIniGeo1.MT.20230523.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_MPI_HiC_2.0/mIniGeo1_1A.yml (view)
species: Inia geoffrensis
specimen: mIniGeo1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/assembly_MPI_HiC_2.0/HLiniGeo1A.fasta.gz
hap2: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/assembly_MPI_HiC_2.0/HLiniGeo1B.fasta.gz
pretext_hap1: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/assembly_MPI_HiC_2.0/mIniGeo1_A.pretext
pretext_hap2: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/assembly_MPI_HiC_2.0/mIniGeo1_B.pretext
kmer_spectra_img: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/assembly_MPI_HiC_2.0/merqury/mIniGeo1_png/
pacbio_read_dir: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/genomic_data/dovetail/
pipeline:
  - hifiasm (0.16.1)
  - yahs (1.1a)
assembled_by_group: Dresden
notes: This was a hifiasm-HiC assembly of mIniGeo1 (Dresden ID is HLiniGeo1), resulting in two complete haplotypes (A and B). HiC scaffolding was performed with yahs. The HiC prep was Dovetail omnic. The specimen was a male mammal. The assembly was performed by Tilman Schell and Michael Hiller. We am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap1. 
assembly_MPI_HiC_2.0/mIniGeo1_2B.yml (view)
species: Inia geoffrensis
specimen: mIniGeo1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/assembly_MPI_HiC_2.0/HLiniGeo1A.fasta.gz
hap2: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/assembly_MPI_HiC_2.0/HLiniGeo1B.fasta.gz
pretext_hap1: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/assembly_MPI_HiC_2.0/mIniGeo1_A.pretext
pretext_hap2: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/assembly_MPI_HiC_2.0/mIniGeo1_B.pretext
kmer_spectra_img: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/assembly_MPI_HiC_2.0/merqury/mIniGeo1_png/
pacbio_read_dir: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Inia_geoffrensis/mIniGeo1/genomic_data/dovetail/
pipeline:
  - hifiasm (0.16.1)
  - yahs (1.1a)
assembled_by_group: Dresden
notes: This was a hifiasm-HiC assembly of mIniGeo1 (Dresden ID is HLiniGeo1), resulting in two complete haplotypes (A and B). HiC scaffolding was performed with yahs. The HiC prep was Dovetail omnic. The specimen was a male mammal. The assembly was performed by Tilman Schell and Michael Hiller. We 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.