Usage

Pssst...

The first steps in order to use this software are installing all it's Dependencies and generating the References it will use when running.

Once those previous steps are taken, you can start analyzing your samples. Take a look at the [Directory Structure]] in order to understand how the analysis output is organized. All the directories of the analysis are created automatically except for ANALYSIS/00-reads, where you should place your raw fastq.gz files. Also all the directories below REFERENCES must be exactly as they appear on the [[Directory Structure]], including the file names. In the [References page you will find all the necessary steps to create the structure.

All set?

Great! So you have made sure you have everything you need to make this run. Let's run it!. The gist of the analysis is as follows:

1. Quality control: trims your reads and makes them neat and beautiful for the next steps of the analysis.
2. Host filtering: filters out all the reads of the host to make the rest of analysis cleaner.
3. Mapping against reference: Maps your reads to the bacteria, virus, fungi or parasite (Invertebrate and Protozoa) reference and saves all those that match.
4. Assembly: Tries to assemble the reads in each group (bacteria, virus, fungi and parasite) to make longer contigs.
5. Blast: Runs blast of each of the contigs generated in the previous step against the corresponding database.
6. Coverage: Calculates the coverage for each of the genomes in the reference and creates depth graphs. Note that the coverage can be calculated immediately after the third step (Mapping).
7. Generating Results

But I want to analyze several samples at once

If you want to analyze several samples you must simply run the Sample Name list generator and then proceed as explained above, using the wrapper scripts explained in each section.