Tree of Life QC

Info

NCBI taxon id: 45351
Order: Actiniaria
Family: Edwardsiidae
NCBI lineage: Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;Edwardsiidae;Nematostella;
GoaT genome size (M): 278 (direct)
GoaT asm span (M): 269 (direct)
GoaT chr no.: 34 (ancestor)
ToLID prefix: jaNemVect

Specimens

Below is information about specimens collected for this species retrieved from the Golden Record manifest.

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public_name
specimen_id
gal
sex
organism_part
biosample
biospecimen
jaNemVect1NHMUK014449091NATURAL HISTORY MUSEUMHERMAPHRODITE_MONOECIOUSWHOLE_ORGANISMSAMEA8534498SAMEA8534429
jaNemVect2NHMUK014449133NATURAL HISTORY MUSEUMHERMAPHRODITE_MONOECIOUSWHOLE_ORGANISMSAMEA8534510SAMEA8534435
jaNemVect3NHMUK014449175NATURAL HISTORY MUSEUMHERMAPHRODITE_MONOECIOUSWHOLE_ORGANISMSAMEA8534520SAMEA8534443
jaNemVect4NHMUK014449219NATURAL HISTORY MUSEUMHERMAPHRODITE_MONOECIOUSWHOLE_ORGANISMSAMEA8534522SAMEA8534445
jaNemVect5NHMUK014449259NATURAL HISTORY MUSEUMHERMAPHRODITE_MONOECIOUSWHOLE_ORGANISMSAMEA8534528SAMEA8534449
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Spectra estimates

Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope.

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source
specimen
k-mer
k-cov
haploid size
repeat (%)
heterozygosity (%)
model fit (%)
model error (%)
histogram
hic-arima2jaNemVect631187.3269,093,28139.260.9394.570.43
pacbiojaNemVect13126.53263,534,79537.920.8296.190.15

Sequence data

PacBio run data

Below are stats for each PacBio seqeuncing run collected for this species.

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pipeline
specimen
date
run id
movie
well
tag
yield
N50
sample accession
run accession
barcode
PacBio - HiFijaNemVect12021-05-1082086m64174e_210510_040930C01101114,698,430,3969,982SAMEA8534498ERR8575398
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Illumina run data

Illumina run stats.

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pipeline
specimen
date
run id
read pairs
yield
sample accession
run accession
run status
barcode
Hi-C - Arima v2jaNemVect62021-10-2341426_2#6947,163,988143,021,762,188SAMEA8534529ERR8571699qc completeNematostella vectensis (1.00)
RNA PolyAjaNemVect52022-08-2345657_1#4048,716,3147,356,163,414SAMEA8534528qc completeNematostella vectensis (1.00)
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Cobionts

Below are results from a screen of the PacBio data using Mash screen against RefSeq assemblies. Only results with identity over 90% are displayed.

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identity
info
0.992899[10804 seqs] NW_001823610.1 Nematostella vectensis NEMVEscaffold_18970 genomic scaffold, whole genome shotgun sequence [...]
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Species composition by small subunit (SSU) presence in the assembly.

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specimen
contig
SSU length
attributed taxonomy by SSU
jaNemVect1atg000665l1775
  • ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;Edwardsiidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;
jaNemVect1atg001183l1804
  • ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;Edwardsiidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;
jaNemVect1atg004204l1799
  • ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;Edwardsiidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;
jaNemVect1atg004491l1799
  • ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;Edwardsiidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;
jaNemVect1atg004734l1809
  • ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;Edwardsiidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;
jaNemVect1atg004976l1803
  • ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;Edwardsiidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;
jaNemVect1atg005234l1799
  • ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;Edwardsiidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;
jaNemVect1atg005632l1779
  • ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;Edwardsiidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;
jaNemVect1atg006551l1799
  • ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;Edwardsiidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;
jaNemVect1atg008253l540
  • ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;
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Re-assembly of reads classified under each identified SSU Marker family.

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specimen
family
classified reads
original assembly
re-assembly
count
(%)
BUSCO
BUSCO
contigs
contig length
reads
BUSCO
contigs
contig length
additional reads
circos
No matching records found

Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.

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specimen
visualisation
jaNemVect1

Canonical tetranucleotide counts for each contig or scaffold reduced to two dimensions with UMAP to allow visualisation.

Features (colours represent quantile bins):

  • Hexamer: Estimated coding density (expected to be higher in microbes than in animals).
  • FastK: The median number of times each 60-mer in the sequence occures across the whole assembly (illustrates repetitiveness)
  • Unique_15mers: Number of unique 15-mers per base pair (illustrates sequence diversity)
  • Is_Connected: Presence of at least one Hi-C connection to another scaffold (absence of connections can indicate contamination)
  • Connections_Base: Number of Hi-C connections per base pair

  • jaNemVect1.hifiasm.20220206

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
jaNemVect1hicanu2022-02-06507,2136,285533,307,080C:95.4%[S:37.2%,D:58.2%],F:2.6%,M:2.0%,n:954Q60.6-C98.9(HiFi)
jaNemVect1hicanu.purging2022-02-061,449,689522268,777,676C:95.1%[S:94.3%,D:0.8%],F:2.5%,M:2.4%,n:954Q59.7-C98.1(HiFi)
jaNemVect1hifiasm2022-02-062,582,139606313,043,356C:95.2%[S:91.3%,D:3.9%],F:2.5%,M:2.3%,n:954Q57.4-C98.8(HiFi)
jaNemVect1hifiasm.purging2022-02-063,331,131218270,493,208C:94.7%[S:94.0%,D:0.7%],F:2.5%,M:2.8%,n:954Q58.3-C98.2(HiFi)
jaNemVect1hifiasm.scaffolding.salsa2022-02-062,849,38123216,600,058131270,543,708C:94.7%[S:94.0%,D:0.7%],F:2.5%,M:2.8%,n:954Q58.3-C98.2(HiFi)
jaNemVect1hifiasm.scaffolding.yahs2022-02-062,927,18922817,626,698105270,517,808C:94.7%[S:94.1%,D:0.6%],F:2.5%,M:2.8%,n:954Q58.3-C98.2(HiFi)

Organelles

In-progress organelle results from MitoHiFi2.

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specimen
asm
date
length
genes
frameshifts
is circular
reference
jaNemVect1hicanu2022-02-0616,38228NoneDQ643835.1; 16,389 bp; 17 genes
jaNemVect1reads2022-02-0616,37429NoneDQ643835.1; 16,389 bp; 17 genes
jaNemVect1hifiasm2022-02-0616,38529ND4DQ643835.1; 16,389 bp; 17 genes
WTSI

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