Folker Meyer: Metagenomic Data Annotation

Folker Meyer Argonne National Laboratory and University of Chicago June 14 th , 1 st EMP meeting Shenzhen, China Metagenome Annotation

Metagenomics needs the magic wand.. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],data Who are they? What are they doing?

Portals help with computational analysis ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

2010 state of metagenomics ,[object Object],[object Object],[object Object],[object Object]

2011: many small scale projects V3 03/2011 ,[object Object],[object Object],[object Object]

Even data upload is hard!  Jumploader Thanks to Rob Knight ’s team to pointing us there 

Part of an emerging digital biology ,[object Object],Source: MG-RAST, 800+ shared metagenomes

Computing cost dominate ,[object Object],Source: Rob Knight, UColorado From: Wilkening et al., IEEE Cluster09, 2009 computing sequencing

Challenges during shotgun metagenome analysis ,[object Object],[object Object],[object Object],[object Object]

Quality control for de-novo sequencing ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Tell me if my data set is of type A or B ,[object Object],[object Object],Real data sets from MG-RAST ,[object Object],[object Object],K. Keegan, in preparation % duplicates varies also

Finding features ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Performance Analysis on simulated data sets w/ errors W. Trimble, in preparation

Characterizing features ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

MG-RAST v3 workflow (simplified) SFF, fastq and fasta data find emPCR and BridgePCR artifacts find coding regions/peptides using FragGeneScan (Ye, NAR 2010) Many databases integrated GSC’s M5nr Upload QC / normalization Similarities (Parallel Blat) Metabolic reconstruction Community reconstruction Metadata Feature prediction (FGS) Abundance profiles Metabolic model

The future ,[object Object],[object Object],[object Object],Source: Rob Knight, UColorado Driving force 600 GBp / run 60 GBp / run

Future 1: World is not clonal, study strain/species variation ,[object Object],new strain? new strain?

Future 2: Expand metadata (1): MIMS/MIMARKS ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Capture metadata Extensive metadata questionnaire supporting offline editors // input

Expand metadata support (2): Capture metadata early Imagine adding metadata to the plot below: Very hard after the fact! capture metadata early Aanensen et al, Plos ONE, 2009

Many current challenges and pitfalls ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Acknowledgements ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Folker Meyer: Metagenomic Data Annotation

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Folker Meyer: Metagenomic Data Annotation