Assembly with preprocessing and SRA download
Associated Tutorial
This workflows is part of the tutorial assembly_with_preprocessing_and_sra_download, available in the GTN
Thanks to...
Tutorial Author(s): Wolfgang Maier
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Assembly and intrahost/low-frequency variant calling for viral samples
Type: Nextflow
Creators: Patel H, Sarai Varona and Sara Monzon, Varona S and Monzon S
Submitter: WorkflowHub Sandbox Bot
Assembly, binning and annotation of metagenomes
Type: Nextflow
Creators: Hadrien Gourlé, No author provided, Daniel Straub, Sabrina Krakau
Submitter: WorkflowHub Sandbox Bot
Galaxy workflow
Type: Galaxy
Creators: Erwan Corre, Stéphanie Robin, Anthony Bretaudeau, Alexandre Cormier
Submitter: Helena Rasche
Galaxy workflow
Type: Galaxy
Creators: Erwan Corre, Stéphanie Robin, Anthony Bretaudeau, Alexandre Cormier, Laura Leroi
Submitter: Helena Rasche
A workflow!
Optional workflow to purge duplicates from the contig assembly.
Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)
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.
DownloadVIRify 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/ ...
Hybrid genome assembly.
Introduction
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
Documentation
The nf-core/denovohybrid pipeline comes with documentation about the pipeline, found in the docs/ directory:
Installation Pipeline configuration
Local installation Adding your own system config Reference genomes
Running the ...
