BecA-ILRI Hub genomics and bioinformatics platforms
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BecA-ILRI Hub genomics and bioinformatics platforms

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Poster prepared by Mark Wamalwa, Francesca Stomeo, Joyce Njuguna and Appolinaire Djikeng, May 2013

Poster prepared by Mark Wamalwa, Francesca Stomeo, Joyce Njuguna and Appolinaire Djikeng, May 2013

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BecA-ILRI Hub genomics and bioinformatics platforms Document Transcript

  • 1. Molecular  Diagnos/cs    •  Development   of   new   diagnos2c   assays   and   epidemiological   surveillance   of   viral  pathogens  of  livestock  and  crops  in  East  and  Central  Africa  using  LAMP  assays  •  East  Coast  fever  (ECF)  recombinant  vaccine  development  •  The  plant  virome  ecology  in  African  farming  systems  Mobilizing biosciences for Africa’s development  BecA-­‐ILRI  Hub  Genomics  and  Bioinforma/cs  Pla=orms  This  document  is  licensed  for  use  under  a  Crea/ve  Commons  ACribu/on-­‐Noncommercial-­‐Share  Alike  3.0  Unported  License                May  2013    Mark  Wamalwa,  Francesca  Stomeo,  Joyce  Njuguna,  Appolinaire  Djikeng.                                                                BecA-­‐ILRI  Hub,  Nairobi,  PO  Box  30709,  00100,  Kenya  (m.wamalwa@cgiar.org)      Highlights  from  projects  using  the  BecA-­‐ILRI  Genomics  and  Bioinforma/cs  Pla=orms      The  BecA-­‐ILRI  Hub  genomics  plaIorm  is  equipped  with  both  capillary  (ABI  3130xl,  ABI  3730xl  and  ABI  3500xl)  and  second-­‐genera2on  sequencing  (the  Roche  454  GSFLX™  Titanium  pyrosequencer  and  Illumina  MiSeq)  plaIorms  integrated  with  high  performance  compu2ng  systems.  The  Bioinforma2cs  plaIorm  leverages  on  the  current  Genomics  plaIorm  to  provide  advanced  computa2onal  services,  access  to  high  performance  compu2ng,  data  storage,  bioinforma2cs  support  and  consultancy  services  to  African  scien2sts  and  external  users.   Bioinforma2cs   offers   tremendous   opportuni2es   and   has   great   poten2al   to   underpin   biotechnological   solu2ons   to   agricultural   development   constraints.   In   a   nutshell,  bioinforma2cs  is  the  key  to  understanding  the  molecule  of  life,  DNA.  Using  these  plaIorms,  the  Hub  has  embarked  on  research  ac2vi2es  including  various  genome  (par2al  and  complete)  sequencing  projects  (cassava  re-­‐sequencing,  viral  genomics  and  metagenomics).  Metagenomics  projects  have  been  par2cularly  informa2ve,  as  they  have  provided  the  tools  to  quickly  scan  the  bacterial  and  viral  communi2es  (pathogenic  and  non-­‐pathogenic)  in  specific  ecosystems  with  the  poten2al  of  applica2ons  to  various  food  value  chains.  Hence  experimental  data  output  has  considerably  grown  in  size  and  complexity.  These  robust  plaIorms  will  significantly  increase  our  ability  to  address  major  issues  related  to  pathogens  discovery,  crops  improvement  and  food  security  and  will  con2nue  to  support  capacity  building  and  services  demands  in  the  BecA  Hub  region  and  beyond.        Capacity  Building    •  Training  workshops:    a)  Introduc2on  to  Molecular  Biology  and  Bioinforma2cs  Workshop  b)  Advanced  Genomics  and  Bioinforma2cs  Workshop  •  MSc  and  PhD  student  projects  hub.africabiosciences.org  Food  security:  Crop  and  livestock  improvement    •  Bacterial  disease  resistance  in  banana  and  enset    •  Late  blight  resistance  in  potato  •  Weevil  resistance  in  sweet  potato  •  Mosaic  virus  resistance  in  cassava.    •  Maize-­‐sorghum  hybrid/molecular  marker  •  Climate-­‐smart  Brachiaria  grasses  for  improving  livestock  produc2on      Key  partners  include  IITA,  CIP,  MARI  (Tanzania),  EIAR  (Ethiopia)  ILRI  Kenya  HPC  Cluster    (88  Nodes)  1.  2.  3.  4.  Quality  Control  Assembly    (De  novo/Reference)  Feature  predic2on  Data  Visualiza2on  Bioinforma/cs  Core  Ac/vi/es    Sta/s/cal  Support  • Experimental  design  Primary  Data  Analysis  • NGS  QC,  spa2al  defect  removal  • 454  GA  Pipleline  Secondary/Downstream  analysis  • Differen2al  Expression  • Structural  varia2on,  geonomic  rearrangements  • SNP  and  CN  analysis  • microRNA  profiling  • GO  enrichment  Training/Capacity  Building  •  Mo2f  Finding  •  Func2onal/Network  Analysis  Data  Management  •  NGS  data  storage  and  manipula2on  •  Data  warehouse  facili2es:  databases  Soaware  development  •  Bioconductor  packages:  NGS  annota2on  packages  •  Automated  NGS  analysis  packages  Bioinforma/cs  tools  •  Ensembl,  Galaxy,  Cytoscape