Strainer: software for analysis of population variation in community genomic datasets.

John M Eppley,Wayne M Getz,Gene W Tyson,Jillian F Banfield

doi:10.1186/1471-2105-8-398

Abstract

BackgroundMetagenomic analyses of microbial communities that are comprehensive enough to provide multiple samples of most loci in the genomes of the dominant organism types will also reveal patterns of genetic variation within natural populations. New bioinformatic tools will enable visualization and comprehensive analysis of this sequence variation and inference of recent evolutionary and ecological processes.ResultsWe have developed a software package for analysis and visualization of genetic variation in populations and reconstruction of strain variants from otherwise co-assembled sequences. Sequencing reads can be clustered by matching patterns of single nucleotide polymorphisms to generate predicted gene and protein variant sequences, identify conserved intergenic regulatory sequences, and determine the quantity and distribution of recombination events.ConclusionThe Strainer software, a first generation metagenomic bioinformatics tool, facilitates comprehension and analysis of heterogeneity intrinsic in natural communities. The program reveals the degree of clustering among closely related sequence variants and provides a rapid means to generate gene and protein sequences for functional, ecological, and evolutionary analyses.

Highlights

Metagenomic analyses of microbial communities that are comprehensive enough to provide multiple samples of most loci in the genomes of the dominant organism types will reveal patterns of genetic variation within natural populations
Some metagenomic studies aim to reconstruct the majority of genomes of the dominant organisms in microbial communities ("community genomics")
Reconstruction of gene variant inventories for specific organisms is a formidable task without tools to visualize and analyze sequence variation in a genomic context. This endeavor will benefit from a new generation of bioinformatics tools enabling comprehensive analyses of the genomic variation at a population level captured in these data

Summary

Results

We have developed a software package for analysis and visualization of genetic variation in populations and reconstruction of strain variants from otherwise co-assembled sequences. Sequencing reads can be clustered by matching patterns of single nucleotide polymorphisms to generate predicted gene and protein variant sequences, identify conserved intergenic regulatory sequences, and determine the quantity and distribution of recombination events

Conclusion

Background

Discussion

Hugenholtz P

19. Pearson WR