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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Amplicon metagenomics

Paired-end only

mothur

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

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its

The QIIME 1.9 ITS pipeline analysis fungal ITS amplicon data using the UNITE reference OTUs (alpha version 12_11).

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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 (new)

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 (new)

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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qiime1 (legacy)

The QIIME 1.9 16S pipeline starts with FASTQ data and finishes with publication-quality figures and statistical results.

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Shotgun metagenomics

Paired-end only

WGSA (new)

The WGSA pipeline uses raw paired end (PE) shotgun metagenomics reads, proceeds to trim, filter, error correct and decontaminate them (from host DNA), then performs de novo read assembly from the PE reads from each sample, to produce biologically informative metagenomic assemblies.

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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)

The pipeline uses as input raw data files and proceeds to trim, align reads and call variants against a SARS-CoV-2 reference.

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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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