Sarcoramphus papa

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bSarPap1 79.69 Gbp N/A 37.4 GiB
Arima bSarPap1 75.69 Gbp N/A 39.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 October 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bSarPap1 PacBio HiFi (.fq) 79.69 Gbp N/A 37.4 GiB
Arima 75.69 Gbp N/A 39.2 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 October 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 11 March 2024
bSarPap1.hap1.cur.20240311.fasta.gz (396.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 233.24 Mbp 1 234.82 Mbp
20 2 103.42 Mbp 2 197.78 Mbp
30 4 54.58 Mbp 3 145.98 Mbp
40 7 51.04 Mbp 4 96.98 Mbp
50 10 40.90 Mbp 6 81.52 Mbp
60 16 23.43 Mbp 8 51.42 Mbp
70 23 18.96 Mbp 11 42.75 Mbp
80 33 11.82 Mbp 16 27.66 Mbp
90 55 5.08 Mbp 24 12.93 Mbp
100 278 11.89 Kbp 124 11.89 Kbp
1.000x 278 1.54 Gbp 124 1.54 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 11 March 2024
bSarPap1.hap2.cur.20240311.fasta.gz (361.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 151.49 Mbp 1 236.91 Mbp
20 3 80.90 Mbp 2 193.07 Mbp
30 5 55.55 Mbp 3 146.96 Mbp
40 8 49.70 Mbp 4 99.02 Mbp
50 11 30.64 Mbp 5 87.06 Mbp
60 17 21.32 Mbp 8 43.20 Mbp
70 25 15.05 Mbp 12 25.78 Mbp
80 38 7.96 Mbp 19 15.46 Mbp
90 63 4.06 Mbp 33 6.43 Mbp
100 269 12.30 Kbp 141 12.30 Kbp
1.000x 269 1.47 Gbp 141 1.47 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 5 January 2024
bSarPap1.MT.20240105.fasta.gz (5.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bSarPap1_hap1.yml (view)
species: Sarcoramphus papa
specimen: bSarPap1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_vgp_HiC_2.0/bSarPap1.HiC.hap1.20240106.fasta.gz
hap2: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_vgp_HiC_2.0/bSarPap1.HiC.hap2.20240106.fasta.gz
pretext_hap1: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bSarPap1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bSarPap1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_vgp_HiC_2.0/evaluation/merqury_postpurge/bSarPap1_png/
pacbio_read_dir: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/genomic_data/arima/
mito: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_MT_rockefeller/bSarPap1.MT.20240105.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bSarPap1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS. The assemblies underwent purge_dups pipeline to reconcile extra 2-copy k-mers in hap2 and missing k-mers in hap1. The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. 
assembly_vgp_HiC_2.0/bSarPap1_hap2.yml (view)
species: Sarcoramphus papa
specimen: bSarPap1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_vgp_HiC_2.0/bSarPap1.HiC.hap1.20240106.fasta.gz
hap2: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_vgp_HiC_2.0/bSarPap1.HiC.hap2.20240106.fasta.gz
pretext_hap1: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/bSarPap1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/bSarPap1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_vgp_HiC_2.0/evaluation/merqury_postpurge/bSarPap1_png/
pacbio_read_dir: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/genomic_data/arima/
mito: s3://genomeark/species/Sarcoramphus_papa/bSarPap1/assembly_MT_rockefeller/bSarPap1.MT.20240105.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of bSarPap1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS. The assemblies underwent purge_dups pipeline to reconcile extra 2-copy k-mers in hap2 and missing k-mers in hap1. The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. 
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.