Loading Input File In Megan

Question

[vijay]

I am using MEGAN metagenome analyzer for analyzing my metagenome sequence data. So far, I am running a standalone blast against 16s sequence database that I have created locally in my system. And I feed the output of this blast as the input to MEGAN(using the "Import from BLAST"option). Though I am able to perform my analyses with this, I just want to know is there any other way through which I could provide input to MEGAN.

Responses are highly appreciated.

-Vijay

Answer 1

[Josh Herr]

If you read the latest version of the MEGAN manual, you see there are numerous ways to import BLAST data into the program. Besides opening the RMA file (MEGAN specific format), you can import data from outside BLAST programs in XML format, SAM files, RDP classifier output files, Silva output files, CSVs from QIIME & MOTHUR, and BIOME files from MG-RAST.

One of the benefits to processing your reads by BLASTing in MEGAN, even if you have analyzed your data elsewhere (and I highly recommend using more than one data analysis program) is the fact that you'll need a synonyms file for MEGAN for database compatibility between your reads and the MEGAN program. This file is needed to visualize your data when importing outside data formats.