GigaScience | Abstract | AXIOME: automated exploration of microbial diversity
From Josh Neufeld's lab this paper describes a series of tools for automation of microbial diversity analyses.
Abstract:
BackgroundAlthough high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research.
FindingsAXIOME streamlines and manages analysis of small subunit (SSU) rRNA marker data in QIIME and mothur. AXIOME also implements features including the PAired-eND Assembler for Illumina sequences (PANDAseq), non-negative matrix factorization (NMF), multi-response permutation procedures (MRPP), exploring and recovering phylogenetic novelty (SSUnique) and indicator species analysis. AXIOME has a companion graphical user interface (GUI) and is designed to be easily extended to facilitate customized research workflows.
ConclusionsAXIOME is an actively developed, open source project written in Vala and available from GitHub (http://neufeld.github.com/axiome) and as a Debian package. Axiometic, a GUI companion tool is also freely available (http://neufeld.github.com/axiometic). Given that data analysis has become an important bottleneck for microbial ecology studies, the development of user-friendly computational tools remains a high priority. AXIOME represents an important step in this direction by automating multi-step bioinformatic analyses and enabling the customization of procedures to suit the diverse research needs of the microbial ecology community.
Workflows like this are what many many people need. I note - I have not used this yet but it looks promising. It has some parallels to the WATERS workflow package that came from my lab a few years ago (see more about it here: http://phylogenomics.wordpress.com/software/waters/.) Alas WATERS is no longer being actively developed. Anyway - AXIOME has additional features and certainly seems like it would be useful to many people.
Odd, I was a reviewer for this paper (has open review which is viewable here: http://www.gigasciencejournal.com/content/2/1/3/prepub) and the last correspondance I had was on Dec. 17. My review was favourable with only discretionary revisions, but still odd that the editor didn't email me with the revisions or that is was accepted?!
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