[2014.08.25] albertsen isme15 cami: why metgenomics is broken
DESCRIPTION
Why metgenomics is brokenTRANSCRIPT
Why metagenomics
is broken
Mads Albertsen, PhD studentSøren M. Karst, Rasmus H. Kirekegaard & Per H. Nielsen
CENTER FOR MICROBIAL COMMUNITIES
CAMI25-08-2014ISME15, Soul, South Korea
@MadsAlbertsen85
slides: goo.gl/xxxxx
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYwww.cami-challenge.org
Critical Assesment of Metagenome Interpretation
Showcase potentials and limitations
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYwww.cami-challenge.org
Critical Assesment of Metagenome Interpretation
Showcase potentials and limitations
The implication of lack of reference genomes on taxonomic classification
The impact of micro-diversity onassembly and
genome completeness metrics
More visualisations, please.
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Sequence
Assemble
Compare to database(BLAST vs. NCBI RefSeq)
Taxonomic Classification(MEGAN)
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
The simplest metagenome in
the world
Accumulibacter (Class Betaproteobacteria) Nitrospira (Class Nitrospira)
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
The simplest metagenome in
the world
Reads Assembly
Remember to correct for read abundance
99%
1 %
50% 50%
Abun
danc
e (%
)
Accumulibacter (Class Betaproteobacteria) Nitrospira (Class Nitrospira)
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYVisualisation: Ray Cloud Browser (S. Boisvert)
Assembly
... of the simplest metagenome in the world
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Coverage (Abundance)Reads: 2x250 bp MiSeqAssembly: CLC [kmer 64]
ANI
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Sequencing
Assembly
Genome Binning
Re-assembly
Manual curation
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYL. Sauder & J. Neufield, University of Waterloo (in prep)
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYL. Sauder & J. Neufield, University of Waterloo (in prep)
Assembly statistics
# Scaffolds 447
Total Mbp 4.46
% GC 33.7
N50 22281
Essential genes 31/29
High-quality draft genome by HMP
standards
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYL. Sauder & J. Neufield, University of Waterloo (in prep)
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYL. Sauder & J. Neufield, University of Waterloo (in prep)
Taxonomic classification of essential genes
Scaffold Length
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYL. Sauder & J. Neufield, University of Waterloo (in prep)
Taxonomic classification of essential genes
Scaffold Length
All A B C# Scaffolds 447 148 135 164
Total Mbp 4.46 1.40 1.48 1.58
% GC 33.7 34.2 34.2 33.5
N50 22281 17655 27290 21230
Essential genes 31/29 26/29 2/29 3/29
High-quality draft genome by HMP
standards
AB
C
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYL. Sauder & J. Neufield, University of Waterloo (in prep)
Abundance
Scaffold Length
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYL. Sauder & J. Neufield, University of Waterloo (in prep)
Abundance
Scaffold Length
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYExample dataset in the R package
ScaffoldTaxonomic
classification
Tetranucleotide frequencies
Presence of key genes or pathways
% GC
Length
Abundance in different samples
Read connections to other scaffolds
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
In situ proximity
mmgenomeA toolbox for reproducible genome
extraction from metagenomes
goo.gl/ohCVPgMadsAlbertsen/mmgenome
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Unknown unkowns“We pray that micro-diversity didn’t compromise
the assembly and hope our key genes are present.”
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
goo.gl/ohCVPg
@MadsAlbertsen85
slides: goo.gl/xxxxxAcknowledgements
J. NeufieldL. Sauder
G.W. Tyson
C. Dorringer H. Daims
P. Hugenholtz
University of Vienna
Per H. NielsenSøren M. KarstRasmus H. KirkegaardSimon J. McIlroy
K. NelsonS. IshiiS. Ishii
A. Loy M. Wagner F. Moeller
T. Rattei
A. Schramm M. Lund
M. KuhlL. Behrendt
M. Sommer C. Munch