Prokaryotic Genome Sequencing and Assembly
Morag Graham, Gary Van Domselaar and Paul Stothard
from: Bioinformatics and Data Analysis in Microbiology (Edited by: Özlem Taştan Bishop). Caister Academic Press, U.K. (2014)
Researchers can now readily obtain millions of sequence reads from the genomes of their favourite prokaryotic organisms thanks to the development of next-generation sequencing technologies. Through sequence assembly, it is possible to reconstruct large portions of a genome from the overlapping sequence reads. However, assembly is challenging because the sequence reads are generally quite short and genomes often contain internally repeated segments that may confound the complete reconstruction of a genome from its constituent reads. There are different approaches for addressing these challenges that involve, for example, more advanced assembly tools, reference genome sequences, and directed follow-up sequencing. Regardless of the strategy employed there are many steps and programs involved, and the final outputs need to be annotated and interpreted with the known shortcomings of the data and methodologies in mind read more ...