Tree of Life QC

Info

NCBI taxon id: 41880  NCBI; ENA; GoaT
Order: Pseudoscourfieldiales
Family: Pycnococcaceae
NCBI lineage: Eukaryota;Viridiplantae;Chlorophyta;Pycnococcaceae;Pycnococcus;
GoaT genome size (M): 73 (ancestor)
GoaT asm span (M): 32 (direct)
GoaT chr no.: 20 (ancestor)
GoaT haploid no.: 7 (ancestor)
GoaT ploidy: 38 (ancestor)
ToLID prefix: ucPycProv

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
ucPycProv1SAN0000882SANGER INSTITUTENOT_COLLECTEDWHOLE_ORGANISMSAMEA7524550SAMEA7524508
ucPycProv1SAN0000882SANGER INSTITUTENOT_COLLECTEDWHOLE_ORGANISMSAMEA7524537SAMEA7524508
ucPycProv1SAN0000882SANGER INSTITUTENOT_COLLECTEDWHOLE_ORGANISMSAMEA7524539SAMEA7524508
ucPycProv1SAN0000882SANGER INSTITUTENOT_COLLECTEDWHOLE_ORGANISMSAMEA7524549SAMEA7524508
ucPycProv1SAN0000882SANGER INSTITUTENOT_COLLECTEDWHOLE_ORGANISMSAMEA7524545SAMEA7524508
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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
pacbioucPycProv131218.941,966,3125.142.1365.690.26
histogram.txt
hic-arima2ucPycProv13119.081,887,775,688127.596.1781.460.32
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 - HiFiucPycProv12020-10-2277883m64016_201022_152708A011011741,730,09412,748SAMEA7524508ERR8705848
PacBio - HiFiucPycProv12020-11-2878610m64094_201128_210619C01101119,217,028,69213,209SAMEA7524508ERR8705849
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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
Hi-C - Arima v2ucPycProv12021-07-3039559_2#2655,934,82099,046,157,820SAMEA7524508ERR8571632qc completePycnococcus provasolii (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
0.977643NZ_CP003984.1 Planktomarina temperata RCA23, complete genome
0.969782[33 seqs] NZ_FOSM01000032.1 Celeribacter marinus strain DSM 100036, whole genome shotgun sequence [...]
0.95314[26 seqs] NZ_GG657907.1 Methylophaga thiooxydans DMS010 genomic scaffold scf_1104571000292, whole genome shotgun sequence [...]
0.925333[44 seqs] NZ_LZFQ01000001.1 Donghicola sp. JL3646 contig1, whole genome shotgun sequence [...]
0.921831NC_015554.1 Alteromonas sp. SN2, complete genome
0.912148[6 seqs] NZ_KI421507.1 Phaeobacter arcticus DSM 23566 genomic scaffold Phaar_neu_scaffold_2516677464.1, whole genome shotgun sequence [...]
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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
No matching records found

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
ucPycProv1

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

    BTK datasets:

    ucPycProv1Pri

    Assemblies

    In-progress assembly QC.

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    specimen
    asm
    date
    contig N50
    contigs
    scaffold N50
    scaffolds
    length
    BUSCO
    merqury
    ucPycProv1hifiasm2021-05-03810,76473192,702,523C:77.3%[S:69.8%,D:7.5%],F:9.8%,M:12.9%,n:255Q51.7-C98.8(HiFi)
    ucPycProv1hicanu2021-05-03691,2841,625142,426,038C:78.1%[S:37.3%,D:40.8%],F:9.8%,M:12.1%,n:255Q65.2-C98.9(HiFi)

    Organelles

    In-progress organelle results from MitoHiFi or Oatk.

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    specimen
    asm
    organelle
    date
    length
    genes
    frameshifts
    is circular
    reference
    No matching records found
    WTSI

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