YABI Workflows for Genomics, Transcriptomics and Metagenomics

Next Generation Sequencing (NGS) affordability has given many smaller biological laboratories the ability to design complex NGS experiments as part of their research. The management and analysis of NGS data however can be problematic in terms of the data set size (commonly hundreds of Gigabytes), computer resources required, and the appropriate choice of tools, parameters and workflows to use. In addition many biologists may not be experienced in running Unix/Linux command line bioinformatics tools. In this case the analysis of NGS data can be a non-trivial task.

In genomics, transcriptomics and metagenomics distinct NGS processing and analytical steps exist. These include quality assessment, quality filtering, sample deconvolution, alignment, assembly and annotation. In this presentation Yabi [1] workflows designed and implemented for genomics, transcriptomics and metagenomics are described by way of example analyses. These include the assembly and annotation of seven major wheat fungal pathogens, and the metagenomic QIIME [2] analysis of N-fixing legume nodules. These analysis workflows highlight simplified NGS data processing and management in a streamlined and controlled bioinformatics environment ideal for downstream comparative and statistical analysis.

References

1.            Hunter AA, Macgregor AB, Szabo TO, Wellington CA, Bellgard MI: Yabi: An online research environment for Grid, High Performance and Cloud computing. Source Code for Biology and Medicine 2012, 7(1).

2.            Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI et al: QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010, 7(5):335-336.