FARAO – The Flexible All-Round Annotation Organizer

A problem with annotating contigs from genomic and metagenomic projects is that there are few tools that allow the visualization of the annotated features, particularly if those features come from different sources. To alleviate this problem, I have (with assistance from Rickard Hammarén and Chandan Pal) over the last years developed a new annotation and read coverage visualization package – FARAO – which we today introduce to the public. FARAO has been used to produce the basis for the the contig annotation figures in my paper on the polluted Indian lake. Storing and visualizing annotation and coverage information in FARAO has a number of advantages. FARAO is able to:

• Integrate annotation and coverage information for the same sequence set, enabling coverage estimates of annotated features
• Scale across millions of sequences and annotated features
• Filter sequences, such that only entries with annotations satisfying certain given criteria will be outputted
• Handle annotation and coverage data produced by a range of different bioinformatics tools
• Handle custom parsers through a flexible interface, allowing for adaption of the software to virtually any bioinformatic tool
• Produce high-quality EPS output
• Integrate with MySQL databases

FARAO is today moved from a private pre-release state to a public beta state. It is still possible that this version contains bug that we have not discovered in our testing. Please send me an e-mail and make us aware of the potential shortcomings of our software if you find any unexpected behavior in this version of FARAO.