Workflows
What is a Workflow?Filters
Simple bacterial assembly and annotation pipeline.
ATACSeq peak-calling and differential analysis pipeline.
Type: Nextflow
Creators: Harshil Patel, Patel H, Langer B, Espinosa-Carrasco J, Syme R
Submitter: WorkflowHub Bot
B/T cell repertoire analysis pipeline with immcantation framework. WIP, currently requires a bunch of changes first.
Type: Nextflow
Creators: Gisela Gabernet, Simon Heumos, Alexander Peltzer
Submitter: WorkflowHub Bot
RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.
Pre-processing of mass spectrometry-based metabolomics data
Tests Importing single-end multiplexed data (not demultiplexed yet)
Type: Galaxy
Creators: Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ
Submitter: WorkflowHub Bot
Use DADA2 for sequence quality control. DADA2 is a pipeline for detecting and correcting (where possible) Illumina amplicon sequence data. As implemented in the q2-dada2 plugin, this quality control process will additionally filter any phiX reads (commonly present in marker gene Illumina sequence data) that are identified in the sequencing data, and will filter chimeric sequences.
Type: Galaxy
Creators: Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ
Submitter: WorkflowHub Bot
dada2 amplicon analysis for paired end data
The workflow has three main outputs:
- the sequence table (output of makeSequenceTable)
- the taxonomy (output of assignTaxonomy)
- the counts which allow to track the number of sequences in the samples through the steps (output of sequence counts)
This workflow performs segmentation and counting of cell nuclei using fluorescence microscopy images. The segmentation step is performed using Otsu thresholding (Otsu, 1979). The workflow is based on the tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html
Assemble long reads with Flye, then view assembly statistics and assembly graph
