Blog Series: Workshop on Genomics, Cesky Krumlov; Preparation--Assembly

Section 4: Assembly

This next section deals with an introduction to assembly and assemblers. All the suggested readings are freely available which is awesome:

1. Birol, I et al., 2009. De novo transcriptome assembly with ABySS. Bioinformatics. 25:2872-2877.
2. Zerbino, DR and E Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18:821-829.
3. Langmead, B. 2010. Aligning short sequencing reads with Bowtie. Current Protocols in Bioinformatics, Chapter 11, Unit 11.7.

There two general ways in which you can compile short reads to make your genome; reference mapping assembly and de novo assembly. There are benefits and caveats to both.

Blog Series: Workshop on Genomics, Cesky Krumlov; Preparation--Genome Structure

Section 2: Genomic Structure

The prep section for genomic structure was small with two articles suggested, one of which you'll need a subscription to read; the other is freely available! Huzzah!

• Alkan, C; BP Coe and EE Eichler. 2011. Genome structural variation discovery and genotyping. Nature Reviews Genetics. 12:363-376. (subscription needed)
• Mills, RE et al., 2011. Mapping copy number variation by population-scale genome sequencing. Nature. 470:59-65. (FREE!)

So lets jump into Mills et al. and learn something...the one caveat to this article is they automatically assume you know what a 'structural variant' is and they are specifically talking about this with respect to the human genome. So lets back-track a little--skim if you're already a structural 'pro'...or better yet, add your two cents in the comments along with other links to clarify this topic.

Blog Series: Workshop on Genomics, Cesky Krumlov; Preparation--Modern Genome Sequencing Technology

Given the workshop will be moving quite quickly the organizer(s) suggested for those of us with less background to do some reading up in certain topics which they outline and include links to on the website in a section called Preparation.

This page, with respect to the workshop on genomics, is broken down into sections. Total there are a suggested 23 readings or websites, unfortunately many (11 of 23) of the links, you have to have a subscription to view the articles beyond the abstract; which unfortunately I do not have and my institution has limited subscriptions; besides most of my preparation is being done at home where I would't have access to the institutional subscriptions anyway. I'll be going section by section with the papers linked and offer some additional suggestions for those unable to access articles due to lack of subscription.