Summer Undergraduate Researcher

Boyce Thompson Institute, Ithaca, NY | June 2012 – August 2012 (3 months)
Diagram showing two-part pipeline for sweet potato virus genome analysis: alignment of known viruses (left) and assembly of novel viral genomes (right).
Pipeline for sweet potato virus genome analysis. The left panel shows alignment of known viral genomes; the right panel illustrates assembly of novel viruses from sequencing data.
View text description of flowchart

Sweet Potato Virus Genome Analysis Pipeline

Step 1: Preprocessing

Clean raw sequencing data by removing barcodes and adapters.

Step 2: Choose Analysis Path

🧭 Alignment Path
  1. Align reads to the virus genome database.
  2. Correct contigs.
  3. Remove redundant sequences.
🧬 Assembly Path
  1. Assemble contigs using Velvet.
  2. BLAST against non-redundant protein sequences.
  3. Compare results back to virus genome contigs.

Summary

Relevant Publications

Determining the pan-African sweetpotato virome: Understanding virus diversity, distribution and evolution and their impacts on sweetpotato production in Africa

Gutierrez, D., Tachin, M., Schulz, S., Miano, D., Ndunguru, J., Mukassa, S., ... & Kreuze, J. F.

CIP Research Report • 2012

References
Boyce Thompson Institute Sweet Potato Virome Velvet Assembler NCBI BLAST Fei Lab

More Work Experiences

Summer Undergraduate Researcher

J. Craig Venter Institute, Rockville, MD | June 2013 – August 2013 (3 months)
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Undergraduate Researcher

Cornell University, Ithaca, NY | June 2012 – August 2012 (3 months)
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