Next generation sequencing is a powerful method increasing in popularity for use in metagenomic and transcriptomic analysis in environmental microbiology. Compared to Sanger sequencing, next generation allows for sequencing of the complete genomic content of a sample without the need to make clone libraries. Using this technique, microbial community analysis can be performed in a matter of days instead of weeks or months.
One problem with next generation sequencing projects is the handling of massive amounts of sequencing data that must be organized, cleaned up, assembled, and analyzed. Sequencing read lengths using the 454/Roche instrument are between 100-400 bp in length and the sequencing of an entire genome can generate millions of pieces of sequence that must be assembled.
For example, researchers at Bielefeld University in Germany used a single sequencing run on the Genome Sequencer FLX system to completely assemble and characterize the genome of Corynebacterium kroppenstedtii. In 7.5 hrs, they generated over 500,000 shotgun reads with greater than 100 million bases that were assembled into a contiguous genomic sequence with a total size of 2,446,804 bp. Can you imagine the bioinformatics required to assemble that much information in one day? It is a primary concern for next generation sequencing labs using this innovative technology for microbial community analysis in rare environmental samples. Easy to use computing programs are desperately needed to make data interpretation manageable and fast.
The purpose of the PANGEA (Pipeline for analysis of next generation amplicons) program is exactly this. This month in the July issue of The ISME Journal (4, 852-861, July 2010), Adriana Giongo from the lab of Eric Triplett at the University of Florida in Gainesville published a study demonstrating the functionality of a new set of computing tools for making analysis of next generation sequencing data faster and easier. PANGEA is written in Perl and can be run on Mac OSX, Windows, or Linux.
To keep reading about PANGEA and get links to the article and source codes for the program, click the Source link.