A wide extent of inter-strain diversity in virulent and vaccine strains of alpha-herpesviruses

Good example on de novo genome assembly, annotation, comparsion

http://genomics-pubs.princeton.edu/prv/scripts.shtml

Overview & Table of Contents

Part I - Pre-Assembly Processing

These steps take raw Illumina^® sequence data and prepare it for de novo assembly, using a series of quality-controls and filters.

Part II - De novo Assembly & Genome Finishing

This phase of genome production takes high-quality short sequence reads, and by homology-based overlaps, joins them into longer and longer pieces.

Part III - Quality Assessment of New Genomes

These steps assess the quality of the assembly and address any inconsistencies. These scripts function in conjunction with wet-bench analyses, such as restriction fragment length polymorphism (RFLP) analysis and directed PCR validations.

Part IV - Annotation & Genome Comparison

This phase involves annotation, curation, and comparison of multiple genome sequences to reveal interesting biological features.

Addendum - Relevant Websites and Lists of Scripts Used

All scripts used are freely available online (web links provided) or are available here (see Downloads link on left) for download and free use.