Gavialis gangeticus

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


Resource Primary Assembly Alternate Assembly
GenBank rGavGan2: GCA_030020295.1 rGavGan2: GCA_030020385.1
ENA rGavGan2: GCA_030020295.1 rGavGan2: GCA_030020385.1
UCSC Genome Browser rGavGan2: GCA_030020295.1 rGavGan2: GCA_030020385.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rGavGan2 81.67 Gbp N/A 65.9 GiB
Bionano rGavGan2 N/A N/A 1.3 GiB
Arima rGavGan2 248.86 Gbp N/A 122.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rGavGan2 PacBio HiFi (.fq) 81.67 Gbp N/A 65.9 GiB
Bionano N/A N/A 1.3 GiB
Arima 248.86 Gbp N/A 122.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 May 2022.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 6 April 2023
rGavGan2.hap1.decon.20230406.fasta.gz (673.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 124.84 Mbp 1 472.07 Mbp
20 4 112.17 Mbp 1 472.07 Mbp
30 7 90.48 Mbp 2 311.80 Mbp
40 9 87.62 Mbp 3 299.52 Mbp
50 12 73.46 Mbp 4 255.85 Mbp
60 15 68.41 Mbp 5 217.72 Mbp
70 19 53.50 Mbp 6 100.53 Mbp
80 24 44.09 Mbp 9 76.55 Mbp
90 33 16.58 Mbp 12 60.93 Mbp
100 359 6.02 Kbp 298 6.02 Kbp
1.000x 359 2.34 Gbp 298 2.34 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 6 April 2023
rGavGan2.hap2.cur.20230406.fasta.gz (673.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 158.96 Mbp 1 473.29 Mbp
20 4 123.37 Mbp 1 473.29 Mbp
30 5 120.64 Mbp 2 312.45 Mbp
40 8 106.03 Mbp 3 299.94 Mbp
50 10 84.24 Mbp 4 257.32 Mbp
60 13 61.01 Mbp 5 217.94 Mbp
70 18 47.11 Mbp 6 101.81 Mbp
80 23 33.53 Mbp 9 84.24 Mbp
90 33 17.07 Mbp 12 71.32 Mbp
100 278 1.00 Kbp 160 1.00 Kbp
1.000x 278 2.33 Gbp 160 2.33 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/rGavGan2_hap2.yml (view)
species: Gavialis gangeticus
specimen: rGavGan2
projects: 
  - vgp
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Gavialis_gangeticus/rGavGan2/assembly_vgp_HiC_2.0/rGavGan2.HiC.hap1.20230202.fasta.gz
hap2: s3://genomeark/species/Gavialis_gangeticus/rGavGan2/assembly_vgp_HiC_2.0/rGavGan2.HiC.hap2.20230202.fasta.gz
pretext_hap1: s3://genomeark/species/Gavialis_gangeticus/rGavGan2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rGavGan2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Gavialis_gangeticus/rGavGan2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rGavGan2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Gavialis_gangeticus/rGavGan2/assembly_vgp_HiC_2.0/evaluation/merqury/rGavGan2_png/
pacbio_read_dir: s3://genomeark/species/Gavialis_gangeticus/rGavGan2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Gavialis_gangeticus/rGavGan2/genomic_data/pacbio_hifi/
hic_read_dir: s3://genomeark/species/Gavialis_gangeticus/rGavGan2/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1+galaxy3)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of rGavGan2, resulting in two complete haplotypes. This individual had bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The kmer spectra indicates a homogametic specimen. We are submitting haplotype 2 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.