Part 5: Exploring your single cell genome

Now that you are fairly confident about the quality of your assembled single cell genome, you are going to have a look at the actual content of the assembly using the program MEGAN. MEGAN is a tool to visualize taxonomic and functional annotations identified through BLAST searches. It parses BLAST results and uses special algorithms and NCBI taxonomy to assign lineages to sequences with BLAST hits. This is useful for various reasons. It can be quite overwhelming to view result outputs from BLAST searches of metagenomic data, which can be very big usually. MEGAN condenses the output from these searches in a manageable view, summarizing sequence data into taxonomic groups. This makes it easier to compare large metagenomic data sets and associated functional annotations.

5.1 Contamination analysis in MEGAN
5.2 Functional analysis in MEGAN

The questions are listed for the two parts separately, just follow the above links.