Narcine bancroftii

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) sNarBan1 2478.17 Gbp N/A 4.2 TiB
PacBio HiFi (.fq) sNarBan1 119.75 Gbp N/A 98.2 GiB
PacBio HiFi (.bam) sNarBan1 382.10 Gbp N/A 1.3 TiB
Arima sNarBan1 329.51 Gbp N/A 162.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 June 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
sNarBan1 PacBio HiFi (subreads) 2478.17 Gbp N/A 4.2 TiB
PacBio HiFi (.fq) 119.75 Gbp N/A 98.2 GiB
PacBio HiFi (.bam) 382.10 Gbp N/A 1.3 TiB
Arima 329.51 Gbp N/A 162.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 11 June 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 1 February 2024
sNarBan1.hap1.cur.20240201.fa.gz (872.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 12 20.30 Mbp 1 494.49 Mbp
20 34 12.77 Mbp 2 376.16 Mbp
30 65 9.26 Mbp 3 375.66 Mbp
40 105 7.32 Mbp 4 321.49 Mbp
50 160 5.20 Mbp 5 257.71 Mbp
60 234 3.91 Mbp 6 254.62 Mbp
70 338 2.63 Mbp 8 179.66 Mbp
80 497 1.64 Mbp 10 108.75 Mbp
90 771 0.87 Mbp 13 94.86 Mbp
100 2038 7.73 Kbp 595 14.41 Kbp
1.000x 2038 3.33 Gbp 595 3.33 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 1 February 2024
sNarBan1.hap2.cur.20240201.fa.gz (834.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 11 20.69 Mbp 1 495.10 Mbp
20 34 11.55 Mbp 2 375.47 Mbp
30 64 9.07 Mbp 3 371.29 Mbp
40 105 6.66 Mbp 4 305.06 Mbp
50 159 5.01 Mbp 5 258.89 Mbp
60 234 3.53 Mbp 6 258.43 Mbp
70 336 2.55 Mbp 7 204.90 Mbp
80 491 1.58 Mbp 9 127.42 Mbp
90 757 0.84 Mbp 12 87.82 Mbp
100 1952 228 bp 445 18.69 Kbp
1.000x 1952 3.11 Gbp 445 3.11 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 16 May 2023
sNarBan1.MT.20230516.fasta.gz (5.7 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/sNarBan1.yml (view)
species: Narcine bancroftii
specimen: sNarBan1
projects: 
  - vgp
data_location: S3
release_to: S3
hap1: s3://genomeark/species/Narcine_bancroftii/sNarBan1/assembly_vgp_HiC_2.0/sNarBan1.HiC.hap1.20230516.fasta.gz
hap2: s3://genomeark/species/Narcine_bancroftii/sNarBan1/assembly_vgp_HiC_2.0/sNarBan1.HiC.hap2.20230516.fasta.gz
pretext_hap1: s3://genomeark/species/Narcine_bancroftii/sNarBan1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/sNarBan1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Narcine_bancroftii/sNarBan1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/sNarBan1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Narcine_bancroftii/sNarBan1/assembly_vgp_HiC_2.0/evaluation/merqury/sNarBan1_png/
mito: s3://genomeark/species/Narcine_bancroftii/sNarBan1/assembly_MT_rockefeller/sNarBan1.MT.20230516.fasta.gz
mito_gb: s3://genomeark/species/Narcine_bancroftii/sNarBan1/assembly_MT_rockefeller/sNarBan1.MT.20230516.gb
pacbio_read_dir: s3://genomeark/species/Narcine_bancroftii/sNarBan1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Narcine_bancroftii/sNarBan1/genomic_data/arima/
pipeline:
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of sNarBan1, 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 assembly was performed on the Galaxy EU servers. 
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.