Open, accessible platform for microbial bioinformatics


Pre-process

Examine and improve the read quality

Analyze

Run an analysis pipeline for your data

Explore

Run additional analysis and visualizations


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survey or shotgun metagenomics

Bacteria

viral (SARS-CoV-2)

COVID

Quality check

Nephele provides a pre-processing quality check pipeline for demultiplexed paired-end and single-end FASTQ files. Please see this FAQ on why you may want to run QC pipeline before you run a microbiome analysis. The Nephele QC pipeline can run a quality control check (FastQC), trim primers and/or adapters, trim and/or filter reads based on quality scores, merge read pairs, and provides summary graphs of the QC steps.

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QC image

Amplicon metagenomics

Paired-end only

mothur

The mothur pipeline only operates on amplicon paired-end FASTQ data.

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Paired-end or Single-end

dada2

The DADA2 pipeline accepts amplicon single or paired-end FASTQ data, and outputs sequence variants, their sample-wise abundances after removing substitution and chimera errors, and summary plots.

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DADA2 ITS

The DADA2 ITS pipeline accepts ITS amplicon FASTQ data, and outputs sequence variants, their sample-wise abundances after removing substitution and chimera errors, and summary plots.

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qiime2

The QIIME 2.0 16S pipeline starts with FASTQ data and finishes with a rarefaction plot, taxonomy barplot and a biom file that can be further explored using the Downstream Analysis pipeline. It relies on VSEARCH for De novo, Open and Closed reference clustering into OTUs. For Single-End data, it also provides the DEBLUR denoising algorithm.

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Shotgun metagenomics

Paired-end only

WGSA2

The WGSA2 pipeline uses raw paired end (PE) shotgun reads to produce de novo assemblies for each sample in a metagenomic dataset, as well as extract optimal levels of information about the taxonomic and functional composition of a microbial community.

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Paired-end or Single-end

WGS - bioBakery

The pipeline runs the Whole Metagenome Shotgun (wmgx) and Visualization for Whole Metagenome Shotgun (wmgx_vis) bioBakery workflows.

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Viral genomics

Paired-end or Single-end

sars-cov-2 (beta)

This pipeline assembles SARS-CoV-2 genome and calls mutations from Illumina sequence data generated using a tiled multiplexed primers strategy (example: Artic protocol). Users can select from primers such as ARTIC and NEB-Varskip. Alternatively, users can upload a custom primers design (in .bed format). See more info below.

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Downstream Analysis: Diversity

You can use biom files from your 16S or ITS pipeline outputs to run the downstream analysis (DA) pipeline. Nephele's DA pipeline uses QIIME 2 to provide sample observation and taxonomic summaries and diversity analyses of an OTU table.

DS graphbar

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Metagenome Inference: PICRUSt2

This pipeline uses PICRUSt2 to predict the functional potential of a community based on marker gene sequencing profiles. It is compatible with the outputs from OTU-picking or denoising algorithm employed in QIIME2 and DADA2 pipelines. The output folder contains inferred genes and protein families and tables of predicted KEGG orthologs (KO), Enzymes (EC) and pathways.

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