Scott Emrich Assistant Professor, Computer Science and Engineering Scientific Manager, VectorBase University of Notre Dame A flexible, scalable genomics.

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Presentation transcript:

Scott Emrich Assistant Professor, Computer Science and Engineering Scientific Manager, VectorBase University of Notre Dame A flexible, scalable genomics framework for integrating heterogeneous vector sequence data

Assembly required…

VectorBase is here to help (esp. –OMICs data) Please see me and/or Dan Lawson (EBI) anytime this meeting

Anopheles gambiae M & S Lawnziak, Emrich et al. (2010, Science)

Some genomic regions display footprint of strong, recent selection Lawniczak, Emrich et al Science

A C G T C G T T A C T G CReference: A C G T C G A T A C T G CSample_1: A C G T C G T T A T T G CSample_2: A C G T C G A T A T T G C A C G T C G A T A C T G C A C G T C G T T A T T G C FlexReseq tool for integrating diverse sequence data

FlexReseq implementation Genome Analysis Toolkit (GATK): Map-Reduce framework that allows efficient access to large resequencing data sets FlexReseq: A module for GATK: Configurable interface allows easy data exploration Modular implementation of rules allows for easy extension of software Saves you from lots of scripting (Perl) code! McKenna et al., Genome Research, 2010

A malaria use-case for FlexReseq Samarakoon, Regier, et al., BMC Genomics, 2011 Why are some parasites drug-resistant? Goal: we want to connect genotype (genome) to phenotype (drug response) How did drug-resistance evolve?

1. Whole genome shotgun sequencing 2. Reference genome mapping NCBI Trace Archive [28] Reference genome (3D7) Parental genomes [shotgun libraries] Progeny genomes [shotgun libraries] PlasmoDB (v5.4) [27] Mapped: SSAHA2 anger.ac.uk Parents HB3, Dd2 Progeny recombinants SC05 7C126 Shotgun libraries GS-FLX technology 454/Roche Genetic cross Wellems et al [24]

A more detailed map of P. falciparum Dd2HB3 Chromosome position Chromosom e (A) 7C126(B) SC05

Association of 2La with clines of aridity in Nigeria… Modified from Coluzzi et al (1979) 24,000 mosquitoes 194 sampling localities

High-throughput sequencing Data from Besansky lab Illumina Genome Analyzer 4 population pools (S-form) SHRiMP alignment BWA works also C. Cheng et al, unpublished

Differential mapping biases do exist

Population haplotyping

In situ error isolation Has been shown to be important in ancient DNA-based ecology

Thanks to… VectorBase (NIH/NIAID) Dr. Nora Besansky (ND) Dr. Frank Collins (ND) Rory Carmichael, Andrew Shehan, Nate Konopinski, Dave Campbell (ND), others… Notre Dame Bioinformatics Lab, Summer 2010 Anopheles genome cluster group i5K Arthropod Genomics Consortium steering committee