Workflows
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Type: Nextflow
Creator: Andreas Wilm, October SESSIONS, Paola Florez DE SESSIONS, ZHU Yuan, Shuzhen SIM, CHU Wenhan Collins, Ignacio
Submitter: Bert Droesbeke
Downloadnfcore/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
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
BioExcel building blocks workflow used in the COVID-19 research
