introduction to metagenomics data analysis - ueb-vhir - 2013
DESCRIPTION
UEB-VHIR's Metagenomics Training. Session 1. 2013/08/26. An Introduction to Metagenomics Data Analysis. Ferran Briansó ([email protected])TRANSCRIPT
An Introduction to An Introduction to Metagenomics Data AnalysisMetagenomics Data Analysis
Metagenomics TrainingMetagenomics Training
Ferran BriansóFerran Briansó
VHIR - 26/08/2013
[email protected]@vhir.org
OutlineOutline
Introduction to Metagenomics
Basic Terminology
Computational Approaches & Tools Whole Genome Shotgun 16S/ITS Community Surveys
Recommended Tools MEGAN mothur QIIME AXIOME & CloVR
Introduction to METAGENOMICSMETAGENOMICS
IntroductionIntroduction
First use of the term metagenome, referencing the idea that a collection of genes sequenced from the environment could be analyzed in a way analogous to the study of a single genome.
Handelsman, J.; Rondon, M. R.; Brady, S. F.; Clardy, J.; Goodman, R. M. (1998). "Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products".Chemistry & Biology 5 (10): R245–R249. doi:10.1016/S1074-5521(98)90108-9. PMID 9818143
First use of the term metagenome, referencing the idea that a collection of genes sequenced from the environment could be analyzed in a way analogous to the study of a single genome.
“The application of modern genomics techniques to the study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species.”
Handelsman, J.; Rondon, M. R.; Brady, S. F.; Clardy, J.; Goodman, R. M. (1998). "Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products".Chemistry & Biology 5 (10): R245–R249. doi:10.1016/S1074-5521(98)90108-9. PMID 9818143
Chen, K.; Pachter, L. (2005). "Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities".PLoS Computational Biology 1 (2): e24. doi:10.1371/journal.pcbi.0010024
IntroductionIntroduction
Source: US Division of Earth & Life Studies of the National Academieshttp://dels-old.nas.edu/metagenomics/overview.shtml
IntroductionIntroduction
Source: US Division of Earth & Life Studies of the National Academieshttp://dels-old.nas.edu/metagenomics/overview.shtml
IntroductionIntroduction
Source:
IntroductionIntroduction
Source: Feng Chen, JGI
IntroductionIntroduction
Perfomance Comparison for (some) Platforms
Basic TERMINOLOGYTERMINOLOGY
TerminologyTerminology
Trimming: is the pre-processing step of cleaning sequence data (primers, multiplexing barcodes...) from automated DNA sequencers prior to sequence assembly and other downstream uses.
Binning is the process of grouping reads or contigs and assigning them to operational taxonomic units (OTUs).
OTU (Operational Taxonomic Unit): Taxonomic level of sampling selected by the user to be used in a study. Typically using a percent sequence similarity threshold for classifying microbes within the same, or different, OTUs.
Trimming: is the pre-processing step of cleaning sequence data (primers, multiplexing barcodes...) from automated DNA sequencers prior to sequence assembly and other downstream uses.
Binning is the process of grouping reads or contigs and assigning them to operational taxonomic units (OTUs).
OTU (Operational Taxonomic Unit): Taxonomic level of sampling selected by the user to be used in a study. Typically using a percent sequence similarity threshold for classifying microbes within the same, or different, OTUs.
Chimeras: Artificial sequences formed during PCR amplification. The majority of them are believed to arise from incomplete extension. During subsequent cycles of PCR, a partially extended strand can bind to a template derived from a different but similar sequence. This then acts as a primer that is extended to form a chimeric sequence (Smith et al. 2010, Thompson et al., 2002, Meyerhans et al., 1990, Judo et al., 1998, Odelberg, 1995). A chimeric template is created during one round, then amplified by subsequent rounds to produce chimeric amplicons that are difficult to distinguish from amplicons derived from a single biological sequence.
TerminologyTerminology
Trimming: is the pre-processing step of cleaning sequence data (primers, multiplexing barcodes...) from automated DNA sequencers prior to sequence assembly and other downstream uses.
Binning is the process of grouping reads or contigs and assigning them to operational taxonomic units (OTUs).
OTU (Operational Taxonomic Unit): Taxonomic level of sampling selected by the user to be used in a study. Typically using a percent sequence similarity threshold for classifying microbes within the same, or different, OTUs.
Chimeras: Artificial sequences formed during PCR amplification. The majority of them are believed to arise from incomplete extension. During subsequent cycles of PCR, a partially extended strand can bind to a template derived from a different but similar sequence. This then acts as a primer that is extended to form a chimeric sequence (Smith et al. 2010, Thompson et al., 2002, Meyerhans et al., 1990, Judo et al., 1998, Odelberg, 1995). A chimeric template is created during one round, then amplified by subsequent rounds to produce chimeric amplicons that are difficult to distinguish from amplicons derived from a single biological sequence.
Alpha diversity: the diversity within a particular area or ecosystem; expressed by the number of species (i.e., species richness) in that ecosystem, or by one or more diversity indices.
Beta diversity: a comparison of of diversity between ecosystems, usually measured as the amount of species change between the ecosystems.
Gamma diversity: a measure of the overall diversity within a large region. Geographic-scale species diversity according to Hunter (2002:448).
TerminologyTerminology
Trimming: is the pre-processing step of cleaning sequence data (primers, multiplexing barcodes...) from automated DNA sequencers prior to sequence assembly and other downstream uses.
Binning is the process of grouping reads or contigs and assigning them to operational taxonomic units (OTUs).
OTU (Operational Taxonomic Unit): Taxonomic level of sampling selected by the user to be used in a study. Typically using a percent sequence similarity threshold for classifying microbes within the same, or different, OTUs.
Chimeras: Artificial sequences formed during PCR amplification. The majority of them are believed to arise from incomplete extension. During subsequent cycles of PCR, a partially extended strand can bind to a template derived from a different but similar sequence. This then acts as a primer that is extended to form a chimeric sequence (Smith et al. 2010, Thompson et al., 2002, Meyerhans et al., 1990, Judo et al., 1998, Odelberg, 1995). A chimeric template is created during one round, then amplified by subsequent rounds to produce chimeric amplicons that are difficult to distinguish from amplicons derived from a single biological sequence.
Alpha diversity: the diversity within a particular area or ecosystem; expressed by the number of species (i.e., species richness) in that ecosystem, or by one or more diversity indices.
Beta diversity: a comparison of of diversity between ecosystems, usually measured as the amount of species change between the ecosystems.
Gamma diversity: a measure of the overall diversity within a large region. Geographic-scale species diversity according to Hunter (2002:448).
Rarefaction allows the calculation of species richness for a given number of individual samples, based on the construction of so-called rarefaction curves. This curve is a plot of the number of species as a function of the number of samples.
TerminologyTerminology
Computational APPROACHES & TOOLSAPPROACHES & TOOLS
Approaches & ToolsApproaches & Tools
Approaches & ToolsApproaches & Tools
Approaches & ToolsApproaches & Tools
Approaches & ToolsApproaches & Tools
Whole Genome SHOTGUNSHOTGUN
Whole Genome ShotgunWhole Genome Shotgun
WGS WorkflowWGS Workflow
WGS WorkflowWGS Workflow
WGS WorkflowWGS Workflow
WGS WorkflowWGS Workflow
Examples of WGS ToolsExamples of WGS Tools
Examples of WGS ToolsExamples of WGS Tools
Analysis of 16S/ITS 16S/ITS Community SurveysCommunity Surveys
16S/ITS community surveys16S/ITS community surveys
16S/ITS issues16S/ITS issues
16S/ITS workflow16S/ITS workflow
16S/ITS workflow16S/ITS workflow
16S/ITS workflow16S/ITS workflow
16S/ITS workflow16S/ITS workflow
Some recommended ToolsTools
Some (recommended) ToolsSome (recommended) Tools
mothur
MEGAN
MEGANMEGAN
2007 →
2011 →
...
...
2012 →
MEGAN 4 for 16S rRNAMEGAN 4 for 16S rRNA
MEGAN 4 for 16S rRNAMEGAN 4 for 16S rRNA
mothurmothur
2009 →
mothurmothur
2009 →
QIIMEQIIME
Integrative Tools/PlatformsTools/Platforms
AXIOMEAXIOME
AXIOMEAXIOME
AXIOMEAXIOME
CloVRCloVR
CloVRCloVR
CloVRCloVR
CloVRCloVR
CloVRCloVR
Ferran BriansóFerran BriansóMGTraining 26/08/2013
Thanks for your attentionThanks for your attention
[email protected]@vhir.org
An Introduction to An Introduction to Metagenomics Data AnalysisMetagenomics Data Analysis
more info at http://ueb.vhir.org/MGT