Macrochelys suwanniensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) rMacSuw1 1845.30 Gbp N/A 3.1 TiB
PacBio HiFi (.fq) rMacSuw1 81.20 Gbp N/A 62.3 GiB
PacBio HiFi (.bam) rMacSuw1 250.47 Gbp N/A 871.1 GiB
Dovetail Genomics rMacSuw1 626.70 Gbp N/A 319.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 September 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rMacSuw1 PacBio HiFi (subreads) 1845.30 Gbp N/A 3.1 TiB
PacBio HiFi (.fq) 81.20 Gbp N/A 62.3 GiB
PacBio HiFi (.bam) 250.47 Gbp N/A 871.1 GiB
Dovetail Genomics 626.70 Gbp N/A 319.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 18 September 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 17 June 2023
rMacSuw1.hap1.cur.20230617.fasta.gz (623.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 125.41 Mbp 1 345.74 Mbp
20 4 92.81 Mbp 2 261.81 Mbp
30 6 71.11 Mbp 3 201.11 Mbp
40 10 52.69 Mbp 4 145.24 Mbp
50 14 43.88 Mbp 5 139.68 Mbp
60 19 32.50 Mbp 7 126.33 Mbp
70 26 27.59 Mbp 9 103.85 Mbp
80 37 15.23 Mbp 11 87.05 Mbp
90 61 4.79 Mbp 16 25.05 Mbp
100 656 12.98 Kbp 366 12.98 Kbp
1.000x 656 2.13 Gbp 366 2.13 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 17 June 2023
rMacSuw1.hap2.cur.20230617.fasta.gz (567.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 100.40 Mbp 1 335.30 Mbp
20 4 83.73 Mbp 2 255.90 Mbp
30 7 58.42 Mbp 2 255.90 Mbp
40 11 42.15 Mbp 3 196.07 Mbp
50 17 28.40 Mbp 5 133.16 Mbp
60 25 20.08 Mbp 6 126.88 Mbp
70 40 9.12 Mbp 8 99.96 Mbp
80 69 5.72 Mbp 10 85.92 Mbp
90 121 2.09 Mbp 14 33.01 Mbp
100 560 18.44 Kbp 199 18.44 Kbp
1.000x 560 1.94 Gbp 199 1.94 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_HiC_2.0/rMacSuw1_hap1.yml (view)
species: Macrochelys suwanniensis
specimen: rMacSuw1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/assembly_vgp_HiC_2.0/rMacSuw1.HiC.hap1.20230407.fasta.gz
hap2: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/assembly_vgp_HiC_2.0/rMacSuw1.HiC.hap2.20230407.fasta.gz
pretext_hap1: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rMacSuw1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rMacSuw1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/assembly_vgp_HiC_2.0/evaluation/merqury/rMacSuw1_png/
pacbio_read_dir: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of rMacSuw1, 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. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap1.
assembly_vgp_HiC_2.0/rMacSuw1_hap2.yml (view)
species: Macrochelys suwanniensis
specimen: rMacSuw1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/assembly_vgp_HiC_2.0/rMacSuw1.HiC.hap1.20230407.fasta.gz
hap2: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/assembly_vgp_HiC_2.0/rMacSuw1.HiC.hap2.20230407.fasta.gz
pretext_hap1: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rMacSuw1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rMacSuw1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/assembly_vgp_HiC_2.0/evaluation/merqury/rMacSuw1_png/
pacbio_read_dir: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Macrochelys_suwanniensis/rMacSuw1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of rMacSuw1, 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. 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.