How-to

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Note: This content is being ported to the new WikiBook project: http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)/De_novo_assembly

Previous contributors should ensure they take proper credit for their work here: http://en.wikibooks.org/w/index.php?title=Next_Generation_Sequencing_(NGS)/Authors


Practicalities: Short, task-oriented articles or tutorials that compare the major tools in the areas of de-novo genome assembly, de-novo transcriptome assembly, sequence alignment, and SNP calling methodologies. These task oriented pages explain commonly used software along with advantages, potential problems and technical requirements. This how-to section serves as a primer for novice bioinformaticians

Technical and Algorithms details: See the references listed in each application section.


How do you do...

Scaffolding 
Provides a description and guideline about the few stand alone scaffolding programs that are available
Exome sequencing analysis 
A first glance of how to analyze exome data using common analysis tools


How do you do... (migrated)

De novo assembly 
From sequencing reads to a genome
De novo transcript assembly 
From sequencing reads to a catalogue of transcripts and gene-set
RNASeq analysis 
From raw reads to differential expression. Provides an overview over some software packages, includes a complete workflow from raw reads to differentially expressed genes
Short read aligners 
BWA, SHRiMP, Bowtie, etc, Which one to use?
SNP detection 
Provides an overview over some of the software packages that can be used for SNP calling
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