Alligator mississippiensis

American alligator

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Alligator mississippiensis
  individuals:
  - short_name: rAllMis1
  short_name: rAllMis
  taxon_id: 8496
  common_name: American alligator
  genome_size: 2518000000
  genome_size_method: GoAT
  order:
    name: Crocodylia
  family:
    name: Alligatoridae
  project: [ vgp ]
CC BY-SA 3.0 H. Zell (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) rAllMis1 1808.02 Gbp 718.04x 3.1 TiB
rAllMis2 380.48 Gbp 151.10x 685.5 GiB
PacBio HiFi (.fq) rAllMis1 90.31 Gbp 35.86x 73.2 GiB
rAllMis2 80.14 Gbp 31.82x 62.9 GiB
PacBio HiFi (.bam) rAllMis1 274.33 Gbp 108.95x 0.9 TiB
rAllMis2 96.81 Gbp 38.45x 339.1 GiB
Arima rAllMis1 185.28 Gbp 73.58x 95.5 GiB
rAllMis2 171.59 Gbp 68.14x 86.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.52 Gbp.
Last upload on 6 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rAllMis1 PacBio HiFi (subreads) 1808.02 Gbp 718.04x 3.1 TiB
PacBio HiFi (.fq) 90.31 Gbp 35.86x 73.2 GiB
PacBio HiFi (.bam) 274.33 Gbp 108.95x 0.9 TiB
Arima 185.28 Gbp 73.58x 95.5 GiB
rAllMis2 PacBio HiFi (subreads) 380.48 Gbp 151.10x 685.5 GiB
PacBio HiFi (.fq) 80.14 Gbp 31.82x 62.9 GiB
PacBio HiFi (.bam) 96.81 Gbp 38.45x 339.1 GiB
Arima 171.59 Gbp 68.14x 86.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.52 Gbp.
Last upload on 6 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 14 April 2023
rSteOdo1.hap1.decon.20230414.fasta.gz (688.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 104.00 Mbp 1 481.29 Mbp
20 5 91.95 Mbp 2 307.84 Mbp
30 9 58.20 Mbp 2 307.84 Mbp
40 13 47.25 Mbp 3 304.93 Mbp
50 19 38.97 Mbp 4 256.32 Mbp
60 26 32.96 Mbp 5 221.19 Mbp
70 36 21.29 Mbp 7 101.56 Mbp
80 50 13.56 Mbp 10 77.99 Mbp
90 84 2.69 Mbp 13 67.96 Mbp
100 0 0
0.941x 806 2.37 Gbp 670 2.37 Gbp
NG based on genome size 2.52 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 14 April 2023
rSteOdo1.hap2.cur.20230414.fasta.gz (678.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 129.54 Mbp 1 486.60 Mbp
20 5 78.28 Mbp 2 307.64 Mbp
30 9 54.97 Mbp 2 307.64 Mbp
40 14 41.12 Mbp 3 303.74 Mbp
50 21 36.48 Mbp 4 255.08 Mbp
60 28 30.27 Mbp 5 220.92 Mbp
70 37 23.89 Mbp 7 90.02 Mbp
80 51 13.56 Mbp 11 75.95 Mbp
90 93 2.46 Mbp 15 38.74 Mbp
100 0 0
0.925x 355 2.33 Gbp 194 2.35 Gbp
NG based on genome size 2.52 Gbp.
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 28 August 2024
rAllMis2.HiC.hap1.20240828.fasta.gz (682.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 110.83 Mbp 1 476.30 Mbp
20 5 70.82 Mbp 2 305.08 Mbp
30 9 51.85 Mbp 2 305.08 Mbp
40 14 44.34 Mbp 3 303.17 Mbp
50 20 36.46 Mbp 4 255.31 Mbp
60 27 33.15 Mbp 5 220.95 Mbp
70 37 20.82 Mbp 8 83.46 Mbp
80 50 15.69 Mbp 11 74.23 Mbp
90 87 2.56 Mbp 15 36.63 Mbp
100 0 0
0.935x 453 2.36 Gbp 342 2.36 Gbp
NG based on genome size 2.52 Gbp.
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 28 August 2024
rAllMis2.HiC.hap2.20240828.fasta.gz (682.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 93.54 Mbp 1 0.77 Gbp
20 5 78.26 Mbp 1 0.77 Gbp
30 9 65.81 Mbp 1 0.77 Gbp
40 14 47.41 Mbp 2 305.71 Mbp
50 20 38.55 Mbp 3 255.48 Mbp
60 27 34.26 Mbp 4 220.86 Mbp
70 35 26.91 Mbp 7 83.76 Mbp
80 49 14.71 Mbp 10 75.68 Mbp
90 83 3.43 Mbp 14 39.51 Mbp
100 0 0
0.930x 253 2.34 Gbp 148 2.34 Gbp
NG based on genome size 2.52 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/rSteOdo1_hap2.yml (view)
species: Sternotherus odoratus
specimen: rSteOdo1
projects: 
  - vgp
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/assembly_vgp_HiC_2.0/rSteOdo1.HiC.hap1.20230208.fasta.gz
hap2: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/assembly_vgp_HiC_2.0/rSteOdo1.HiC.hap2.20230208.fasta.gz
pretext_hap1: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rSteOdo1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rSteOdo1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/assembly_vgp_HiC_2.0/evaluation/merqury/rSteOdo1_png/
pacbio_read_dir: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Sternotherus_odoratus/rSteOdo1/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1+galaxy4)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of rSteOdo1, 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. MitoHiFi was run on the raw reads, but a full mitogenome could not be recovered. 
assembly_vgp_HiC_2.0/rAllMis2.yml (view)
species: Alligator mississippiensis
specimen: rAllMis2
projects: 
  - vgp
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Alligator_mississippiensis/rAllMis2/assembly_vgp_HiC_2.0/rAllMis2.HiC.hap1.20240828.fasta.gz
hap2: s3://genomeark/species/Alligator_mississippiensis/rAllMis2/assembly_vgp_HiC_2.0/rAllMis2.HiC.hap2.20240828.fasta.gz
pretext_hap1: s3://genomeark/species/Alligator_mississippiensis/rAllMis2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rAllMis2_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Alligator_mississippiensis/rAllMis2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rAllMis2_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Alligator_mississippiensis/rAllMis2/assembly_vgp_HiC_2.0/evaluation/merqury/rAllMis2_png/
pacbio_read_type: hifi
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of rAllMis2, resulting in two complete haplotypes. The HiC data was Arima v2 using the Swift-IDT library prep kit. The assembly was performed on usegalaxy.eu infrastructure by Saim Momin. The data for this individual was originally named rAllMis1, but has been renamed to rAllMis2. 
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.