Mergus octosetaceus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bMerOct1 1177.43 Gbp N/A 2.0 TiB
PacBio HiFi (.fq) bMerOct1 56.77 Gbp N/A 41.6 GiB
PacBio HiFi (.bam) bMerOct1 172.93 Gbp N/A 595.4 GiB
Arima bMerOct1 133.38 Gbp N/A 70.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 July 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bMerOct1 PacBio HiFi (subreads) 1177.43 Gbp N/A 2.0 TiB
PacBio HiFi (.fq) 56.77 Gbp N/A 41.6 GiB
PacBio HiFi (.bam) 172.93 Gbp N/A 595.4 GiB
Arima 133.38 Gbp N/A 70.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 26 July 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 26 January 2024
bMerOct1.hap1.cur.20240126.fasta.gz (345.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 25.97 Mbp 1 216.68 Mbp
20 10 21.83 Mbp 2 170.47 Mbp
30 16 17.21 Mbp 2 170.47 Mbp
40 24 13.22 Mbp 3 125.30 Mbp
50 34 10.80 Mbp 5 83.84 Mbp
60 48 8.17 Mbp 6 66.85 Mbp
70 66 5.63 Mbp 10 29.22 Mbp
80 97 2.64 Mbp 15 21.83 Mbp
90 171 0.93 Mbp 22 11.94 Mbp
100 895 671 bp 568 12.91 Kbp
1.000x 895 1.25 Gbp 568 1.25 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 26 January 2024
bMerOct1.hap2.cur.20240126.fasta.gz (325.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 28.23 Mbp 1 221.79 Mbp
20 9 24.26 Mbp 2 178.44 Mbp
30 14 19.39 Mbp 2 178.44 Mbp
40 22 13.45 Mbp 3 131.79 Mbp
50 32 10.49 Mbp 4 77.73 Mbp
60 45 8.37 Mbp 7 38.20 Mbp
70 62 6.17 Mbp 10 28.62 Mbp
80 89 3.20 Mbp 16 18.05 Mbp
90 171 0.72 Mbp 28 3.20 Mbp
100 964 1.57 Kbp 720 17.06 Kbp
1.000x 964 1.21 Gbp 720 1.21 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 12 May 2023
bMerOct1.MT.20230512.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bMerOct1_hap1.yml (view)
species: Mergus octosetaceus
specimen: bMerOct1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_vgp_HiC_2.0/bMerOct1.HiC.hap1.20230516.fasta.gz
hap2: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_vgp_HiC_2.0/bMerOct1.HiC.hap2.20230516.fasta.gz
pretext_hap1: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bMerOct1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bMerOct1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_vgp_HiC_2.0/evaluation/merqury/bMerOct1_png/
mito: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_MT_rockefeller/bMerOct1.MT.20230512.fasta.gz
mito_gb: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_MT_rockefeller/bMerOct1.MT.20230512.gb
pacbio_read_dir: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/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 bMerOct1, 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. The kmer spectra indicate a heterogametic specimen, and the sample metadata indicates a female bird. I am submitting both hap1 & hap2 for dual curation. This is the curation ticket for hap1. 
assembly_vgp_HiC_2.0/bMerOct1_hap2.yml (view)
species: Mergus octosetaceus
specimen: bMerOct1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_vgp_HiC_2.0/bMerOct1.HiC.hap1.20230516.fasta.gz
hap2: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_vgp_HiC_2.0/bMerOct1.HiC.hap2.20230516.fasta.gz
pretext_hap1: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bMerOct1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bMerOct1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_vgp_HiC_2.0/evaluation/merqury/bMerOct1_png/
mito: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_MT_rockefeller/bMerOct1.MT.20230512.fasta.gz
mito_gb: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/assembly_MT_rockefeller/bMerOct1.MT.20230512.gb
pacbio_read_dir: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Mergus_octosetaceus/bMerOct1/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 bMerOct1, 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. The kmer spectra indicate a heterogametic specimen, and the sample metadata indicates a female bird. 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.