Open, accessible platform for microbial bioinfomatics


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

Metagenomics

viral (SARS-CoV-2)

Viral

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 Learn more

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Metagenomics

mothur

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

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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. Learn more

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qiime1

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

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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. Learn more

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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). Learn more

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wgs

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

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Viral

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. Learn more

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Downstream analysis

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. Learn more

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