Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data

Background: The advent of pyrophosphate sequencing makes large volumes of sequencing data available at a lower cost than previously possible. However, the short read lengths are difficult to assemble and the large dataset is difficult to handle. During the sequencing of a virus from the tsetse fly, Glossina pallidipes, we found the need for tools to search quickly a set of reads for near exact text matches. Methods: A set of tools is provided to search a large data set of pyrophosphate sequence reads under a "live" CD version of Linux on a standard PC that can be used by anyone without prior knowledge of Linux and without having to install a Linux setup on the computer. The tools permit short lengths of de novo assembly, checking of existing assembled sequences, selection and display of reads from the data set and gathering counts of sequences in the reads. Results: Demonstrations are given of the use of the tools to help with checking an assembly against the fragment data s...

• Type: Journal
• Year: 2008
• Where: SCFBM
• Authors: Nicolas J. Parker, Andrew G. Parker
• Keywords: SCFBM 2008, Sequencing, Short Read Lengths, Tools