What it does

Applies the LCA alignment to reads and can also perform KEGG classification. The input is a BLAST file or something similar. This wrapper supports the following formats for the input Blast file. The SAM, Tabular and Text formats can be produced by The Galaxy MALT Analyzer tool. When these formats are used, this tool will apply the SAM, BlastText and BlastTab format options required by MEGAN.

• Direct Access Archive (DAA) - a proprietary file format developed by PowerISO Computing for disk image files
• BlastXML - XML output from Blast
• Sequence Alignment/Map (SAM) - a tab-delimited text format consisting of a header section, which is optional, and an alignment section
• Tabular - information presented in the form of a table with rows and columns
• Text - plain text format

The tool produces a text file for the LCA alignment.

If the option to Map reads to KEGG KOs is selected, an additional text file containing the KEGG classification is produced. The KEGG database provides a collection of metabolic pathways and other pathways, but due to KEGG licensing restrictions, the Community Edition of KEGG (used by this tool) ships with an early 2011 version of the KEGG classification, so KEGG pathways cannot be viewed in the putput.

The KEGG classification can be displayed as a tree. Genes are mapped onto so-called KO groups and these are present in one or more pathways. The MEGAN program will attempt to map each read onto a gene that has a valid KO identifier and thus, to one or more pathways.

To perform this analysis, MEGAN uses a mapping of GI numbers to KO groups. Hence, if a KEGG-based analysis is desired, then the database that is used in the BLAST alignment must contain GI numbers.