Overview: Nephele is a cloud platform developed by a team of computational biologists and bioinformaticians that also perform metagenomics analysis in collaboration with researchers at NIAID. It was born from the need of making tools and pipelines available to those with limited computational resources or those lacking expertise in metagenomics pipeline development.
Before you use Nephele, you should know that the team has designed the user interface in a series of steps to help guide users through the order of steps recommended for analysis of most datasets. These steps are:
Step 1: Pre-process
We recommend that you always start by inspect the quality of your sequencing data and then proceed to pre-process it (e.g. trim, filter by quality, adapter removal). The Quality Check pipeline available in this Step 1 will inspect and then prepare reads for input to the analysis pipelines. Even though certain analysis pipelines available on Step 2 include a default quality filtering and even a pair merging step, users might prefer to run these ahead of time using this pipeline. If you have already done a quality check of your data and are comfortable with the quality of your reads, proceed to Step 2 and start analyzing your data.
Step 2: Analyze
This step has a growing collection of compute-intensive pipelines that will generate tables of sequence variants, run metagenomics assemblies, assign taxonomy and more. Ideally, the input data has already been examined using the tools available in the Step 1 QC pipeline; remember "Garbage in, Garbage out". The output of some of the pipelines consist of tables and graphics but not everything ends there. Users should download the output files, extract knowledge and also use some of those files (e.g. biom, fasta) as input for other pipelines in the Step 3: Explore section.
Step 3: Explore
In this section users will find pipelines to extract further insights from the data after having completed the processing and analysis. These pipelines will run various analyses and create publication quality graphics.
Please select the analysis you are interested in. Nephele provides amplicon analysis (16S, ITS), WGS metagenomics analysis and Viral (SARS-CoV-2 mapping).
Nephele supports the following data types for analysis types.
Select the type appropriate to your data (e.g. Paired End FASTQ) and click “Next”.
Nephele provides five methods to upload input files: my computer, Google Drive, BaseSpace, Globus and FTP. Upload from my computer allows you to upload files from your local computer. This method is suitable for up to 2GB per fastq or fastq.gz file per file. We recommend that you upload compressed .gz files for performance. Select this option if you are using a sample dataset with small files. If you have a large data set, we recommend opting to use Globus, FTP, Google Drive or BaseSpace method.
After uploading your input files, Nephele pipelines require a mapping file. To upload your mapping file, simply click Browse, select your mapping file, and click Upload. Upload the sample mapping file (xx.xlsx).
Nephele validates your mapping file instantly so that you can correct any error interactively. In order to prevent any mapping file errors, we recommend that you start with mapping file templates provided on the map file upload page for the pipeline you're running.
If you have an error in your mapping file, for example, a typo in your fastq file name column, here is an example of how to correct it using the interactive error page.
Notes on map file validation:
After uploading mapping file and pass the validation, you can select a pipeline. Simply click "Select" on the pipeline you wish to use.
You can learn more about pipelines in Nephele in the Nephele Pipelines section.
Once you select a pipeline, you will see a submission page. You can enter a description of your job so that you can identify different jobs easily.
On this page, there are different tabs such as "Pre-processing" and "Analysis" (dependent on the pipeline) which allow you to change the parameters the pipeline is run with. Don’t forget to have a look if you are interested in different options. See Nephele's Pipeline Section for more details regarding parameters.
Finally, click Validate and Submit!
Congratulations! You have submitted a job! You will receive a Pipeline Started email shortly.
You can resubmit a job without uploading all of your input files again.
Step 1: Enter the Nephele JobID that you would like to resubmit.
Step 2: As long as your job hasn't expired, your input data will be retrieved. The rest of steps are the same as submitting a job. You can re-upload a mapping file and change parameters for the resubmission.