Hyperolius riggenbachi

Riggenbach's reed frog

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


metadata.yaml (view) (edit on github)
species:
  name: Hyperolius riggenbachi
  individuals:
  - short_name: aHypRig1
  short_name: aHypRig
  taxon_id: 752182
  common_name: Riggenbach's reed frog
  genome_size: 4287000000
  genome_size_method: GoAT
  order:
    name: Anura
  family:
    name: Hyperoliidae
  project: [ vgp ]
CC BY 2.5 Václav Gvoždík (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) aHypRig1 579.38 Gbp 135.15x 1.4 TiB
PacBio HiFi (.fq) aHypRig1 184.61 Gbp 43.06x 148.3 GiB
PacBio HiFi (.bam) aHypRig1 46.30 Gbp 10.80x 189.5 GiB
Arima aHypRig1 871.56 Gbp 203.30x 421.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.29 Gbp.
Last upload on 2 August 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aHypRig1 PacBio HiFi (subreads) 579.38 Gbp 135.15x 1.4 TiB
PacBio HiFi (.fq) 184.61 Gbp 43.06x 148.3 GiB
PacBio HiFi (.bam) 46.30 Gbp 10.80x 189.5 GiB
Arima 871.56 Gbp 203.30x 421.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 4.29 Gbp.
Last upload on 2 August 2024.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 8 July 2024
aHypRig1.pri.cur.20240708.fasta.gz (1.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 45 7.53 Mbp 1 0.69 Gbp
20 111 5.67 Mbp 2 0.58 Gbp
30 197 4.40 Mbp 3 0.52 Gbp
40 304 3.64 Mbp 3 0.52 Gbp
50 434 3.00 Mbp 4 0.50 Gbp
60 588 2.53 Mbp 5 451.03 Mbp
70 774 2.10 Mbp 6 392.57 Mbp
80 1000 1.71 Mbp 7 327.69 Mbp
90 1279 1.35 Mbp 9 299.53 Mbp
100 1659 0.93 Mbp 10 296.99 Mbp
1.147x 3516 4.92 Gbp 477 4.92 Gbp
NG based on genome size 4.29 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 8 July 2024
aHypRig1.alt.cur.20240708.fasta.gz (2.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 39 7.75 Mbp 39 7.94 Mbp
20 103 5.95 Mbp 103 5.96 Mbp
30 185 4.72 Mbp 184 4.74 Mbp
40 284 4.01 Mbp 283 4.01 Mbp
50 398 3.54 Mbp 397 3.54 Mbp
60 526 3.18 Mbp 524 3.19 Mbp
70 669 2.82 Mbp 667 2.82 Mbp
80 829 2.53 Mbp 828 2.54 Mbp
90 1009 2.23 Mbp 1007 2.24 Mbp
100 1213 1.99 Mbp 1211 1.99 Mbp
2.265x 14096 9.71 Gbp 14077 9.71 Gbp
NG based on genome size 4.29 Gbp.
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 1 April 2024
aHypRig1.HiC.hap1.20240401.fasta.gz (1.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 44 7.55 Mbp 1 1.47 Gbp
20 109 5.83 Mbp 1 1.47 Gbp
30 194 4.58 Mbp 1 1.47 Gbp
40 298 3.76 Mbp 2 0.56 Gbp
50 423 3.16 Mbp 3 449.62 Mbp
60 572 2.65 Mbp 4 378.39 Mbp
70 750 2.20 Mbp 5 290.32 Mbp
80 965 1.80 Mbp 7 246.89 Mbp
90 1229 1.46 Mbp 8 204.17 Mbp
100 1574 1.04 Mbp 11 157.03 Mbp
1.174x 3554 5.03 Gbp 591 5.03 Gbp
NG based on genome size 4.29 Gbp.
Individual 1 Haplotype 2 Assembly
No assembly available.


Contigs Scaffolds
NG LG Len LG Len
10 - - - -
20 - - - -
30 - - - -
40 - - - -
50 - - - -
60 - - - -
70 - - - -
80 - - - -
90 - - - -
100 - - - -
0.000x - 0.0 Mbp - 0.0 Mbp
Assembly Metadata
assembly_vgp_HiC_2.0/aHypRig1.yml (view)
species: Hyperolius riggenbachi
specimen: aHypRig1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
pri: s3://genomeark/species/Hyperolius_riggenbachi/aHypRig1/assembly_vgp_HiC_2.0/aHypRig1.HiC.hap1.20240401.fasta.gz
alt: s3://genomeark/species/Hyperolius_riggenbachi/aHypRig1/assembly_vgp_HiC_2.0/aHypRig1.HiC.alt.20240401.fasta.gz
pretext: s3://genomeark/species/Hyperolius_riggenbachi/aHypRig1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aHypRig1_hap1_s2.pretext
kmer_spectra_img: s3://genomeark/species/Hyperolius_riggenbachi/aHypRig1/assembly_vgp_HiC_2.0/evaluation/merqury_postpurge/aHypRig1_png/
pacbio_read_dir: s3://genomeark/species/Hyperolius_riggenbachi/aHypRig1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Hyperolius_riggenbachi/aHypRig1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - purge_dups (1.2.6+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of aHypRig1. Merqury and smudgeplot (available in evaluation directories) indicate sample is likely triploid. Results are also in attached PDF. HiC-phasing resulting in two similarly sized assemblies. I then ran purge_dups on hap1 to try to get a haploid representation of the genome. The removed regions were added to hap2, which is now listed on this ticket as an 'alt' assembly. I then used YaHS to scaffold the purged hap1 assembly, which is being submitted as a 'primary' assembly. This is a Phase 1 species (a11). 
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.