This document discusses new tools for surveillance and diagnostics of high priority plant pests. It outlines an optimized next-generation sequencing (NGS) pipeline and data analysis workflow using tools like Bowtie 2, SPADES, BLAST, and SEKT/SAMTOOLS to map reads, assemble genomes de novo, search databases, and call consensus sequences and variants. This NGS approach can differentiate between closely related virus species quickly and accurately.

1. biosecurity built on science
CRC2014 New tools for field grains surveillance and
diagnostics of high priority pests (Linda Zheng)
Evolution of plant virus detection Optimisation of NGS pipeline and NGS data analysis
 Bowtie 2 (reference mapping)
 SPADES (de novo)
 BLAST (database searching)
 SEKT/SAMTOOLS
(consensus/variant calling)
MCDVBYDV PAS? PAV? TuYV? BWYV?
Apply same
pipeline
 Differentiated
between closely
related species
 Fast and accurate