Thank you for choosing Nephele. Here you will find instructions on how to submit a successful job. If you would like to try submitting with a small dataset, below are the sample fastq files and a mapping file.
Note: These data are from a 2017 BioProject in NCBI entitled "Experimental Microbial Dysbiosis Does Not Promote Disease Progression in SIV-Infected Macaques" (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA417022)
|Sequences||72MB||Contains paired-end data (forward and reverse) from 10 samples sequenced on an Illumina MiSeq|
|Mapping File (Excel)||9KB||Metadata file used in Nephele job submissions that describes samples, groups, etc. for analysis|
You can follow along with this user guide using the sample data.
Please select the analysis you are interested in. Nephele provides amplicon analysis including 16S, ITS and WGS metagenomics analysis. Select 16S if you are using the sample data.
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 four methods to upload input files: local, FTP, Google Drive and BaseSpace. Local file upload 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 FTP, Google Drive or BaseSpace method.
Google Drive: We recommend that you organize all of your input files in one folder ahead of time. During upload you will select the folder and all fastq files in that folder will be available for input. Proceed to the next step of uploading the mapping file. Nephele will proceed to import all the fastq files that correspond to the files indicated on the mapping file.
BaseSpace: Nephele will display all available Projects in BaseSpace. During upload you will select the Project you wish to use, Nephele will find all the fastq files associated with that Project. Proceed to the next step of uploading the mapping file. Nephele will proceed to import all the fastq files that correspond to the files indicated on the mapping file.
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.
Select QIIME1 if you use the sample data.
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.