Workflows
What is a Workflow?Filters
Introduction
nfcore/atacseq is a bioinformatics analysis pipeline used for ATAC-seq data.
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.
Pipeline summary
Raw read QC (FastQC) Adapter trimming (Trim Galore!) Alignment (BWA) Mark duplicates (picard) Merge alignments from multiple libraries of the same sample (picard) ...
DownloadA simple bacterial assembly and annotation pipeline
Introduction
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 ...
nf-core/bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
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 / singularity containers making installation trivial and results highly reproducible.
Documentation
The nf-core/bactmap pipeline comes with documentation about the pipeline, found in the docs/ directory:
Installation Pipeline ...
Introduction
The nf-core/bcellmagic pipeline is built to analyze B-cell repertoire sequencing data. It makes use of the Immcantation 2.5.0 toolset and requires targeted sequencing data of the V, D, J and C regions of the B-cell receptor (primers for the V and C genes).
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 ...
nf-core/cageseq
CAGE-seq pipeline.
Introduction
UNDER DEVELOPMENT
This pipeline is currenlty under development. The workflow is not yet finished.
nf-core/cageseq is a pipeline built for the analysis of CAGE-sequencing data.
Analysis steps consist of adapter and artefact trimming (cuatadapt), alignment to a reference (STAR) and CAGE tag counting. Additionally, several quality control steps (FastQC, MultiQC) are included to allow for easy verification of results after a run.
The pipeline is built ...
Introduction
nfcore/chipseq is a bioinformatics analysis pipeline used for Chromatin ImmunopreciPitation sequencing (ChIP-seq) data.
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.
Pipeline summary
Raw read QC (FastQC) Adapter trimming (Trim Galore!) Alignment (BWA) Mark duplicates (picard) Merge alignments from multiple ...
Identifies non-coding RNAs using Rfams covariance models
