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...
- 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