Review Papers On Short Read Mapping?

Question

[Daniel Standage]

I'm teaching a course on computational genome science and next week we're focusing on short read mapping. I'm familiar with and/or have used some of the more popular mapping tools (Bowtie, BWA, Novoalign) as well as related tools for various downstream applications (Tophat/Cufflinks, Novomethyl), so I feel prepared to at least cover the basics. However, I'm curious whether there are any recent review papers that discuss the mapping problem, the various approaches used to solving it, and/or the biological questions scientists are trying to answer with these tools. Any recommendations?

Answer 1

[Botond Sipos]

Nuno A. Fonseca, Johan Rung, Alvis Brazma and John C. Marioni (2012) Tools for mapping high-throughput sequencing data. Bioinformatics 28:3169-3177. doi:10.1093/bioinformatics/bts605

It is quite comprehensive and comes with a regularly updated online compendium of mappers.

[Daniel Standage]

This is exactly what I was looking for. Thanks!

Answer 2

[matted]

• "How to map billions of short reads onto genomes," Trapnell and Salzberg, Nature Biotechnology (2009)
• "A survey of sequence alignment algorithms for next-generation sequencing", Li and Homer, Briefings in Bioinformatics (2010)

They're both slightly dated and don't have the latest and greatest tools, but the motivation and descriptions are still on target. You might complement these reviews with a well-written recent paper like the GEM, bowtie2, or bwa-mem manuscripts.

Answer 3

[Leandro Lima]

A solid quality-control analysis of AB SOLiD short-read sequencing data.

http://www.ncbi.nlm.nih.gov/pubmed/22877770