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

Short read 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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Nanopore quality check

Nephele provides a pre-processing quality check pipeline for Oxford Nanopore Technology (ONT) long read sequences. The Nephele NanoporeQC pipeline runs a quality control check (NanoPlot), trims known or unknown primers and/or adapters (Porechop_abi), trims and/or filters reads (nanoq), 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. Limited to datasets below 2GB zipped.

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Paired-end or Single-end

dada2 recommended

The DADA2 pipeline accepts amplicon single or paired-end FASTQ data, and generates sequence variants with their sample-wise abundances after removing substitution and chimera errors. The pipeline provides rarefaction plots, taxonomy barplots and a biom file for use in the Downstream Analysis pipeline. Also, see Where is QIIME2?

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DADA2 ITS

The DADA2 ITS pipeline accepts ITS amplicon FASTQ data, and generates sequence variants with their sample-wise abundances after removing substitution and chimera errors. The pipeline provides rarefaction plots, taxonomy barplots and a biom file for use in the Downstream Analysis pipeline.

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qiime2/vsearch

The QIIME2/VSEARCH 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 recommended

The WGSA2 pipeline uses paired-end shotgun reads to produce de novo assemblies for each sample in a metagenomic dataset and extract taxonomic and functional information about the microbial community.

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Paired-end or Single-end

WGS - bioBakery

The pipeline runs the BioBakery Whole Metagenome Shotgun (wmgx) for taxonomic profiling and functional annotation, and Visualization for Whole Metagenome Shotgun (wmgx_vis) bioBakery workflows. It is assembly-free.

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Viral genomics

Paired-end or Single-end

sars-cov-2

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.

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Viral metagenomics: DiscoVir

The DiscoVir pipeline uses metagenome assemblies (.fasta files) and sequence alignments (.bam files) to identify viral sequences, taxonomically and functionally characterize the virome, and predict phage hosts.

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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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