Amia calva

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fAmiCal2 49.56 Gbp N/A 22.5 GiB
PacBio HiFi (.bam) fAmiCal2 437.79 Gbp N/A 199.0 GiB
Arima fAmiCal2 55.36 Gbp N/A 29.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fAmiCal2 PacBio HiFi (.fq) 49.56 Gbp N/A 22.5 GiB
PacBio HiFi (.bam) 437.79 Gbp N/A 199.0 GiB
Arima 55.36 Gbp N/A 29.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 21 March 2024.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_curated from 11 January 2024
fAmiCal2.hap1.cur.20240111.fasta.gz (275.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 32.49 Mbp 2 63.57 Mbp
20 7 29.54 Mbp 4 55.60 Mbp
30 10 24.03 Mbp 6 50.67 Mbp
40 15 21.06 Mbp 8 45.55 Mbp
50 20 17.47 Mbp 10 44.18 Mbp
60 26 15.70 Mbp 12 38.05 Mbp
70 34 9.82 Mbp 15 31.21 Mbp
80 47 4.50 Mbp 18 28.15 Mbp
90 79 1.66 Mbp 22 22.84 Mbp
100 486 4.19 Kbp 389 4.19 Kbp
1.000x 486 0.99 Gbp 389 0.99 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_curated from 11 January 2024
fAmiCal2.hap2.cur.20240111.fasta.gz (267.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 52.38 Mbp 2 59.31 Mbp
20 5 32.65 Mbp 4 55.71 Mbp
30 8 26.88 Mbp 5 52.79 Mbp
40 12 25.01 Mbp 7 49.57 Mbp
50 16 20.34 Mbp 10 41.85 Mbp
60 21 16.89 Mbp 12 37.09 Mbp
70 28 10.42 Mbp 15 31.44 Mbp
80 39 8.05 Mbp 18 28.46 Mbp
90 56 3.10 Mbp 21 24.12 Mbp
100 377 11.50 Kbp 297 11.50 Kbp
1.000x 377 0.96 Gbp 297 0.96 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 14 November 2023
fAmiCal2.MT.20231114.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fAmiCal2_hap1.yml (view)
species: Amia calva
specimen: fAmiCal2
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_vgp_HiC_2.0/fAmiCal2.HiC.hap1.20231114.fasta.gz
hap2: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_vgp_HiC_2.0/fAmiCal2.HiC.hap2.20231114.fasta.gz
pretext_hap1: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fAmiCal2_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fAmiCal2_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_vgp_HiC_2.0/evaluation/merqury/fAmiCal2_png/
pacbio_read_dir: s3://genomeark/species/Amia_calva/fAmiCal2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Amia_calva/fAmiCal2/genomic_data/arima/
mito: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_MT_rockefeller/fAmiCal2.MT.20231114.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fAmiCal2, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  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/fAmiCal2_hap2.yml (view)
species: Amia calva
specimen: fAmiCal2
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_vgp_HiC_2.0/fAmiCal2.HiC.hap1.20231114.fasta.gz
hap2: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_vgp_HiC_2.0/fAmiCal2.HiC.hap2.20231114.fasta.gz
pretext_hap1: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fAmiCal2_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fAmiCal2_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_vgp_HiC_2.0/evaluation/merqury/fAmiCal2_png/
pacbio_read_dir: s3://genomeark/species/Amia_calva/fAmiCal2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Amia_calva/fAmiCal2/genomic_data/arima/
mito: s3://genomeark/species/Amia_calva/fAmiCal2/assembly_MT_rockefeller/fAmiCal2.MT.20231114.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fAmiCal2, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  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.