Hyla sarda

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Resource Primary Assembly Alternate Assembly
GenBank aHylSar1: GCA_029493135.1 aHylSar1: GCA_029499605.1
ENA aHylSar1: GCA_029493135.1 aHylSar1: GCA_029499605.1
UCSC Genome Browser aHylSar1: GCA_029493135.1 aHylSar1: GCA_029499605.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aHylSar1 128.55 Gbp 31.04x 89.3 GiB
Bionano aHylSar1 N/A 130.16x 789.2 MiB
Arima aHylSar1 233.47 Gbp 56.36x 114.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.14 Gbp.
Last upload on 2 November 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aHylSar1 PacBio HiFi (.fq) 128.55 Gbp 31.04x 89.3 GiB
Bionano N/A 130.16x 789.2 MiB
Arima 233.47 Gbp 56.36x 114.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.14 Gbp.
Last upload on 2 November 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 8 December 2022
aHylSar1.pri.cur.20221208.fasta.gz (1.1 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 21 14.49 Mbp 0 0.62 Gbp
20 57 9.52 Mbp 1 0.52 Gbp
30 108 6.95 Mbp 2 449.36 Mbp
40 177 5.23 Mbp 3 420.03 Mbp
50 270 3.81 Mbp 4 384.97 Mbp
60 402 2.64 Mbp 5 305.78 Mbp
70 592 1.80 Mbp 6 235.93 Mbp
80 906 0.97 Mbp 8 192.26 Mbp
90 1605 354.43 Kbp 12 50.27 Mbp
100 5770 1.00 Kbp 3473 1.00 Kbp
1.000x 5771 4.14 Gbp 3474 4.14 Gbp
NG based on genome size 4.14 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 8 December 2022
aHylSar1.alt.cur.20221208.fasta.gz (1.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 0 1.16 Mbp 0 1.16 Mbp
20 0 1.16 Mbp 0 1.16 Mbp
30 1 0.99 Mbp 1 0.99 Mbp
40 1 0.99 Mbp 1 0.99 Mbp
50 2 0.84 Mbp 2 0.84 Mbp
60 2 0.84 Mbp 2 0.84 Mbp
70 3 0.64 Mbp 3 0.64 Mbp
80 4 0.59 Mbp 4 0.60 Mbp
90 5 0.55 Mbp 5 0.59 Mbp
100 6 51.56 Kbp 5 0.59 Mbp
1.000x 7 4.81 Mbp 6 4.81 Mbp
NG based on genome size 4.14 Gbp.
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 August 2022
aHylSar1.HiC.hap1.20220806.fasta.gz (1.1 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 21 14.49 Mbp 0 0.89 Gbp
20 57 9.52 Mbp 0 0.89 Gbp
30 108 6.95 Mbp 1 0.60 Gbp
40 178 5.23 Mbp 2 0.51 Gbp
50 271 3.78 Mbp 3 417.68 Mbp
60 404 2.63 Mbp 4 384.13 Mbp
70 595 1.78 Mbp 5 234.42 Mbp
80 913 0.96 Mbp 7 186.61 Mbp
90 1618 351.38 Kbp 54 0.84 Mbp
100 5816 1.00 Kbp 3605 1.00 Kbp
1.000x 5817 4.15 Gbp 3606 4.15 Gbp
NG based on genome size 4.14 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 February 2023
aHylSar1.HiC.hap2.20230206.fasta.gz (1.1 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 23 13.95 Mbp 0 0.61 Gbp
20 58 9.63 Mbp 1 492.44 Mbp
30 106 7.38 Mbp 2 446.74 Mbp
40 170 5.51 Mbp 3 419.94 Mbp
50 257 4.00 Mbp 4 380.64 Mbp
60 376 2.92 Mbp 5 305.48 Mbp
70 548 1.93 Mbp 6 234.46 Mbp
80 820 1.10 Mbp 8 185.86 Mbp
90 1419 400.80 Kbp 13 4.36 Mbp
100 4891 360 bp 2795 1.00 Kbp
1.000x 4892 4.07 Gbp 2796 4.08 Gbp
NG based on genome size 4.14 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/aHylSar1.yml (view)
species: Hyla sarda
specimen: aHylSar1
projects: 
  - vgp
hap1: s3://genomeark/species/Hyla_sarda/aHylSar1/assembly_vgp_HiC_2.0/aHylSar1.HiC.hap1.20220806.fasta.gz
hap2: s3://genomeark/species/Hyla_sarda/aHylSar1/assembly_vgp_HiC_2.0/aHylSar1.HiC.hap2.20220806.fasta.gz
pretext_hap1: s3://genomeark/species/Hyla_sarda/aHylSar1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aHylSar1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Hyla_sarda/aHylSar1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aHylSar1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Hyla_sarda/aHylSar1/assembly_vgp_HiC_2.0/evaluation/aHylSar1_png/
pacbio_read_dir: s3://genomeark/species/Hyla_sarda/aHylSar1/genomic_data/pacbio/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Hyla_sarda/aHylSar1/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Hyla_sarda/aHylSar1/genomic_data/bionano/
pipeline:
  - hifiasm (0.16.1+galaxy2)
  - solve (3.7.0+galaxy0)
  - yahs (1.2a+galaxy1)
assembled_by_group: Rockefeller
notes: Hap1 ( aHylSar1.HiC.hap1.20220806.fasta.gz ) looks more complete based on statistics, but I am including both haplotypes here as we are unsure about if we should curate hap2 instead in order to address the misjoin in the largest scaffold (based on the pretext map). 
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.