Workflows

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125 Workflows visible to you, out of a total of 184
Stable

The tutorial for this workflow can be found on Galaxy Training Network

Type: Galaxy

Creator: Anne Claire Fouilloux

Submitter: Bert Droesbeke

Stable

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.

Type: Nextflow

Creator: Martín Beracochea

Submitter: Laura Rodriguez-Navas

Stable

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.

Type: Common Workflow Language

Creator: Martín Beracochea

Submitter: Laura Rodriguez-Navas

No description specified

Type: Nextflow

Creator: Andreas Wilm, October SESSIONS, Paola Florez DE SESSIONS, ZHU Yuan, Shuzhen SIM, CHU Wenhan Collins, Ignacio

Submitter: Bert Droesbeke

Stable

nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intrahost/low-frequency variant calling for viral samples. The pipeline currently supports metagenomics and amplicon sequencing data derived from the Illumina sequencing platform. This pipeline is a re-implementation of the SARS_Cov2_consensus-nf and SARS_Cov2_assembly-nf pipelines initially developed by Sarai Varona and Sara Monzon from BU-ISCIII. Porting both of these pipelines to nf-core was an international ...

Type: Nextflow

Creator: Alexander Peltzer and Alison Meynert and Edgar Garriga Nogales and Erik Garrison and Gisela Gabernet and Harshil Patel and Joao Curado and Jose Espinosa-Carrasco and Katrin Sameith and Marta Pozuelo and Maxime Garcia and Michael Heuer and Phil Ewels and Simon Heumos and Stephen Kelly and Thanh Le Viet

Submitter: Hervé Ménager

Stable

nf-core/vipr is a bioinformatics best-practice analysis pipeline for assembly and intrahost / low-frequency variant calling for viral samples. 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 / singularity containers making installation trivial and results highly reproducible. Pipeline Steps

Step Main program/s

Trimming, combining of read-pairs per sample and QC Skewer, FastQC

Decontamination ...

Type: Nextflow

Creator: Andreas Wilm, October SESSIONS, Paola Florez DE SESSIONS, ZHU Yuan, Shuzhen SIM, CHU Wenhan Collins

Submitter: Laura Rodriguez-Navas

No description specified

Type: Unrecognized workflow type

Creators: None

Submitter: Stian Soiland-Reyes

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