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
Creator: Andreas Wilm, October SESSIONS, Paola Florez DE SESSIONS, ZHU Yuan, Shuzhen SIM, CHU Wenhan Collins
Submitter: Laura Rodriguez-Navas
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 SARSCov2consensus-nf and SARSCov2assembly-nf pipelines initially developed by Sarai Varona and Sara Monzon from BU-ISCIII. Porting both of these pipelines to nf-core was an international ...
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
Hybrid genome assembly.
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.
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 ...
Creator: Caspar Gross
Submitter: Finn Bacall
A simple bacterial assembly and annotation pipeline
Short Read Assembly
This pipeline is primarily for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using Skewer and performs basic sequencing QC using FastQC. Afterwards, the pipeline performs read assembly using Unicycler. Contamination of the assembly is checked using Kraken2 to verify sample purity.
Long Read Assembly
For users that only have Nanopore data, the pipeline quality ...
Creator: Andreas Wilm, Alexander Peltzer
Submitter: Finn Bacall