Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

ABSTRACT:

Background

De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom.

Results

The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into th

SUBMITTER: Kisand V 

PROVIDER: S-EPMC3618134 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature