Apteryx mantelli

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CC BY-NC 2.0 The.Rohit (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bAptMan1 75.73 Gbp N/A 63.1 GiB
Arima bAptMan1 147.41 Gbp N/A 69.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 9 May 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bAptMan1 PacBio HiFi (.fq) 75.73 Gbp N/A 63.1 GiB
Arima 147.41 Gbp N/A 69.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 9 May 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 4 October 2023
bAptMan1.hap1.cur.20231004.fasta.gz (418.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 48.64 Mbp 1 222.93 Mbp
20 7 35.54 Mbp 2 173.43 Mbp
30 11 31.31 Mbp 3 141.10 Mbp
40 17 24.45 Mbp 4 90.78 Mbp
50 24 19.80 Mbp 6 88.10 Mbp
60 33 15.88 Mbp 9 43.94 Mbp
70 44 10.96 Mbp 13 29.01 Mbp
80 61 6.51 Mbp 19 20.06 Mbp
90 95 2.78 Mbp 29 9.22 Mbp
100 578 7.86 Kbp 408 7.86 Kbp
1.000x 578 1.50 Gbp 408 1.50 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 4 October 2023
bAptMan1.hap2.cur.20231004.fasta.gz (441.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 41.93 Mbp 1 222.81 Mbp
20 8 32.75 Mbp 2 174.30 Mbp
30 13 24.77 Mbp 3 141.87 Mbp
40 20 20.59 Mbp 5 90.88 Mbp
50 29 15.31 Mbp 6 88.13 Mbp
60 40 13.44 Mbp 10 33.35 Mbp
70 54 9.85 Mbp 15 26.82 Mbp
80 74 6.28 Mbp 23 16.08 Mbp
90 113 2.24 Mbp 37 7.35 Mbp
100 504 7.86 Kbp 349 7.86 Kbp
1.000x 504 1.59 Gbp 349 1.59 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 8 August 2023
bAptMan1.MT.20230808.fasta.gz (5.6 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bAptMan1_hap1.yml (view)
species: Apteryx mantelli
specimen: bAptMan1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_vgp_HiC_2.0/bAptMan1.HiC.hap1.20230808.fasta.gz
hap2: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_vgp_HiC_2.0/bAptMan1.HiC.hap2.20230808.fasta.gz
pretext_hap1: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bAptMan1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bAptMan1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_vgp_HiC_2.0/evaluation/merqury/bAptMan1_png/
mito: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_MT_rockefeller/bAptMan1.MT.20230808.fasta.gz
pacbio_read_dir: s3://genomeark/species/Apteryx_mantelli/bAptMan1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Apteryx_mantelli/bAptMan1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bAptMan1, resulting in two complete haplotypes. The provider did not give sex metadata, but the kmer spectra seem to support a homogametic specimen. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. This is a phase 1 species. We are submitting both haplotypes for dual curation, and this is the ticket for hap1. 
assembly_vgp_HiC_2.0/bAptMan1_hap2.yml (view)
species: Apteryx mantelli
specimen: bAptMan1
projects: 
  - vgp
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_vgp_HiC_2.0/bAptMan1.HiC.hap1.20230808.fasta.gz
hap2: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_vgp_HiC_2.0/bAptMan1.HiC.hap2.20230808.fasta.gz
pretext_hap1: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bAptMan1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bAptMan1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_vgp_HiC_2.0/evaluation/merqury/bAptMan1_png/
mito: s3://genomeark/species/Apteryx_mantelli/bAptMan1/assembly_MT_rockefeller/bAptMan1.MT.20230808.fasta.gz
pacbio_read_dir: s3://genomeark/species/Apteryx_mantelli/bAptMan1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Apteryx_mantelli/bAptMan1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of bAptMan1, resulting in two complete haplotypes. The provider did not give sex metadata, but the kmer spectra seem to support a homogametic specimen. This individual did not bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. This is a phase 1 species. We are submitting both haplotypes for dual curation, and this is the 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.