Tree of Life QC

Info

NCBI taxon id: 60958  NCBI; ENA; GoaT
Order: Rhynchobdellida
Family: Piscicolidae
NCBI lineage: Eukaryota;Metazoa;Spiralia;Lophotrochozoa;Annelida;Clitellata;Hirudinea;Hirudinida;Oceanobdelliformes;Piscicolidae;Piscicola;
GoaT genome size (M): 425 (ancestor)
GoaT asm span (M): 171 (direct)
GoaT chr no.: 16 (ancestor)
GoaT haploid no.: 8 (ancestor)
GoaT ploidy: 2 (ancestor)
ToLID prefix: wrPisGeom

Specimens

Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).

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tolid
specimen_id
gal
sex
organism_part
biosample
biospecimen
wrPisGeom1NHMUK014361516NATURAL HISTORY MUSEUMNOT_COLLECTEDWHOLE_ORGANISMSAMEA7521291SAMEA7521191
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Spectra estimates

Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.

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source
specimen
k-mer
k-cov
haploid size
repeat (%)
heterozygosity (%)
model fit (%)
model error (%)
histogram
10xwrPisGeom13133.76343,222,61686.866.7181.251.27
histogram.txt
pacbiowrPisGeom13138.1178,149,54537.271.0094.620.29
histogram.txt
hic-arima2wrPisGeom131269.4155,415,38733.301.6796.070.63
histogram.txt

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 - HiFiwrPisGeom12020-09-1277367m64125_200912_160102C01100314,885,902,35012,635SAMEA7521291ERR9744411
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ONT run data

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

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pipeline
specimen
date
run id
flowcell
type
yield
N50
sample accession
report
No matching records found

Illumina run data

Below are stats for each Illumina run collected for this species. Click on a row to see associated plots from samtools stats.

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pipeline
specimen
date
run id
read pairs
yield
sample accession
run accession
run status
barcode
Chromium genomewrPisGeom12020-11-1635281_7#678,807,90011,899,992,900SAMEA7521291qc completePiscicola geometra (1.00)
Chromium genomewrPisGeom12020-11-1635281_7#772,118,85010,889,946,350SAMEA7521291qc completePiscicola geometra (1.00)
Chromium genomewrPisGeom12020-11-1635281_7#591,248,21413,778,480,314SAMEA7521291qc completePiscicola geometra (1.00)
Chromium genomewrPisGeom12020-11-1635281_7#872,051,74610,879,813,646SAMEA7521291qc completePiscicola geometra (1.00)
Hi-C - Arima v2wrPisGeom12020-10-2135216_5#1841,530,484127,071,103,084SAMEA7521291ERR9767808qc completePiscicola geometra (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
0.95473[4 seqs] NZ_JH815580.1 Aeromonas veronii AER39 supercont1.1, whole genome shotgun sequence [...]
0.932793NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
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Species composition by small subunit (SSU) presence in the assembly with MarkerScan.

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specimen
contig
SSU length
attributed taxonomy by SSU
wrPisGeom1atg003941l1815
  • ENA: Eukaryota;Metazoa;Lophotrochozoa;Annelida;Clitellata;Hirudinea;Hirudinida;Oceanobdelliformes;Piscicolidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Lophotrochozoa;Annelida;Clitellata;Hirudinida;Rhynchobdellida;
wrPisGeom1ptg000030c1501
  • ENA: Bacteria;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Rickettsiaceae;Rickettsia;
wrPisGeom1ptg000129l1527
  • ENA: Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Alcaligenaceae;Achromobacter;
  • SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Burkholderiales;Alcaligenaceae;
wrPisGeom1ptg000236l2191
  • ENA: Eukaryota;Euglenozoa;Kinetoplastida;Trypanosomatidae;Trypanosoma;
  • SILVA: Eukaryota;Discoba;Discicristata;Euglenozoa;Kinetoplastea;Metakinetoplastina;Trypanosomatida;Trypanosoma;
wrPisGeom1ptg000245l2199
  • ENA: Eukaryota;Euglenozoa;Kinetoplastida;Trypanosomatidae;Trypanosoma;
  • SILVA: Eukaryota;Discoba;Discicristata;Euglenozoa;Kinetoplastea;Metakinetoplastina;Trypanosomatida;Trypanosoma;
wrPisGeom1ptg000291c1498
  • ENA: Bacteria;environmental samples;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Holosporales;Holosporaceae;uncultured;
wrPisGeom1ptg000736l2190
  • ENA: Eukaryota;Euglenozoa;Kinetoplastida;Trypanosomatidae;Trypanosoma;
  • SILVA: Eukaryota;Discoba;Discicristata;Euglenozoa;Kinetoplastea;Metakinetoplastina;Trypanosomatida;Trypanosoma;
wrPisGeom1ptg000845l2196
  • ENA: Eukaryota;Euglenozoa;Kinetoplastida;Trypanosomatidae;Trypanosoma;
  • SILVA: Eukaryota;Discoba;Discicristata;Euglenozoa;Kinetoplastea;Metakinetoplastina;Trypanosomatida;Trypanosoma;
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MarkerScan cobiont assembly by read separation based on observed families (see above). These reads are both aligned to the assembly and independently re-assembled. The quality of these assemblies is assessed by their completeness according to BUSCO, their span and the number of reads they encompass. For more information here.

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specimen
family
classified reads
original assembly
re-assembly
count
(%)
BUSCO
BUSCO
contigs
contig length
number of reads
BUSCO
contigs
contig length
number of reads
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
wrPisGeom1

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

  • wrPisGeom1.hifiasm.20220412

BTK datasets:

wrPisGeom1Pri

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
wrPisGeom1hicanu2020-10-15466,9903,664432,837,072-
wrPisGeom1hicanu.purging2020-10-15865,4621,043202,244,151-
wrPisGeom1hicanu.scaff.salsa2020-10-15785,5081,0516,928,121418202,552,959-
wrPisGeom1hicanu.purging_252020-10-15865,4621,043202,362,678-
wrPisGeom1hicanu.repurging2020-10-151,053,160438180,290,300-
wrPisGeom1hifiasm.purging_e2020-10-261,832,7368411,832,736823200,845,667-
wrPisGeom1hifiasm.purging2020-10-261,832,736826203,602,412C:82.8%[S:78.7%,D:4.1%],F:5.8%,M:11.4%,n:978-
wrPisGeom1hifiasm.scaff.salsa2020-10-261,753,7258347,388,889361203,826,104-
wrPisGeom1hifiasm.purging_252020-10-261,801,613832204,571,360-
wrPisGeom1hifiasm2020-10-261,352,1441,338236,657,719C:83.2%[S:75.3%,D:7.9%],F:5.3%,M:11.5%,n:978-
wrPisGeom1hifiasm.repurging2020-10-261,832,736825202,811,967-
wrPisGeom1hifiasm.purging2021-07-221,525,907790205,920,083C:77.4%[S:71.4%,D:6.0%],F:8.4%,M:14.2%,n:954Q37.2-C56.8(10X); Q51.9-C98.8(HiFi)
wrPisGeom1hifiasm2021-07-221,139,8581,326243,946,648C:77.4%[S:65.0%,D:12.4%],F:8.5%,M:14.1%,n:954Q36.7-C57.4(10X); Q51.8-C99.1(HiFi)
wrPisGeom1hifiasm.scaff_.salsa2022-04-121,123,6885007,589,004216211,769,108-
wrPisGeom1hifiasm.scaff_.yahs2022-04-121,161,4985068,272,861334211,661,508-
wrPisGeom1hifiasm.purging2022-04-121,219,847489211,547,640C:77.7%[S:71.4%,D:6.3%],F:8.3%,M:14.0%,n:954Q36.6-C61.9(10X); Q51.2-C98.6(HiFi)
wrPisGeom1hifiasm2022-04-12750,5671,898411,797,916C:79.0%[S:20.6%,D:58.4%],F:7.9%,M:13.1%,n:954Q35.9-C63.3(10X); Q51.2-C99.1(HiFi)
wrPisGeom1hifiasm.purging_2022-04-121,219,847489211,627,108-
wrPisGeom1hifiasm.scaffolding.salsa2022-04-121,123,6885006,853,822223211,686,140C:78.0%[S:71.7%,D:6.3%],F:8.1%,M:13.9%,n:954Q36.6-C61.9(10X); Q51.2-C98.6(HiFi)
wrPisGeom1hifiasm.scaffolding.yahs2022-04-121,161,4985048,272,861331211,582,240C:78.0%[S:71.7%,D:6.3%],F:8.1%,M:13.9%,n:954Q36.6-C61.9(10X); Q51.2-C98.6(HiFi)
wrPisGeom1hicanu2021-07-22478,8063,574431,037,438C:78.0%[S:10.8%,D:67.2%],F:8.1%,M:13.9%,n:954Q38.0-C57.8(10X); Q59.4-C99.4(HiFi)
wrPisGeom1hicanu.purging2021-07-22809,3091,062203,843,664C:77.3%[S:71.4%,D:5.9%],F:8.1%,M:14.6%,n:954Q37.9-C57.0(10X); Q59.0-C99.2(HiFi)
wrPisGeom1hicanu2022-04-12448,4444,750496,605,999C:78.9%[S:7.8%,D:71.1%],F:8.1%,M:13.0%,n:954Q34.8-C42.8(10X); Q56.9-C100.0(HiFi)
wrPisGeom1hicanu.purging2022-04-12999,568794216,142,654C:77.9%[S:70.9%,D:7.0%],F:8.3%,M:13.8%,n:954Q36.6-C62.3(10X); Q56.6-C99.0(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

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specimen
asm
organelle
date
length
genes
frameshifts
is circular
reference
wrPisGeom1mitohifi.hifiasmmito2022-04-1225,02637NoneFalseBK059172.1; 14,788 bp; 37 genes
wrPisGeom1mitohifi.hicanumito2022-04-1225,17237NoneTrueBK059172.1; 14,788 bp; 37 genes
wrPisGeom1mitohifi.readsmito2022-04-1223,93837NoneFalseBK059172.1; 14,788 bp; 37 genes
WTSI

Tree of Life Species Report is developed within the Tree of Life Programme at the Wellcome Sanger Institute
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