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.