Workflow for running LotuS2 tool on fungal ITS paired-end sequencing data, to identify the fungi present in the samples

Associated Tutorial

This workflows is part of the tutorial Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2, available in the GTN

Features

• Includes [Galaxy Workflow ...

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Associated Tutorial

This workflows is part of the tutorial Workflow 3: Functional Information (quick), available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks

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Assembly and intrahost/low-frequency variant calling for viral samples

Assembly, binning and annotation of metagenomes

A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.

16S rRNA amplicon sequencing analysis workflow using QIIME2.

[![GitHub Actions CI ...

VIRify is a recently developed pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies. The pipeline is part of the repertoire of analysis services offered by MGnify. VIRify’s taxonomic classification relies on the detection of taxon-specific profile hidden Markov models (HMMs), built upon a set of 22,014 orthologous protein domains and referred to as ViPhOGs.

VIRify is a recently developed pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies. The pipeline is part of the repertoire of analysis services offered by MGnify. VIRify’s taxonomic classification relies on the detection of taxon-specific profile hidden Markov models (HMMs), built upon a set of 22,014 orthologous protein domains and referred to as ViPhOGs.

Assembly, binning and annotation of metagenomes.

Introduction

This pipeline is for assembly, binning and annotation of metagenomes. It supports both short and long reads, quality trims the reads and adapters with https://github.com/OpenGene/fastp and https://github.com/rrwick/Porechop and performs basic QC with https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.

The pipeline then:

assigns taxonomy to reads using https://ccb.jhu.edu/software/centrifuge/ and/or https://ccb.jhu.edu/software/kraken2/ ...

Introduction

nfcore/ampliseq is a bioinformatics analysis pipeline used for 16S rRNA amplicon sequencing data.

The workflow processes raw data from FastQ inputs (FastQC), trims primer sequences from the reads (Cutadapt), imports data into QIIME2, generates amplicon sequencing variants (ASV, DADA2), classifies features against the SILVA v132 database, excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta ...