Workflows
What is a Workflow?Filters
Workflow (hybrid) metagenomic assembly and binning
- Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
- FastQC (control)
- fastp (quality trimming)
- kraken2 (taxonomy)
- bbmap contamination filter
- Workflow Longread Quality:
- NanoPlot (control)
- filtlong (quality trimming)
- kraken2 (taxonomy)
- minimap2 contamination filter
- Kraken2 taxonomic classification of FASTQ reads
- SPAdes/Flye (Assembly)
- Pilon/Medaka/PyPolCA (Assembly polishing)
- QUAST (Assembly ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Changlin Ke
Submitter: Bart Nijsse
gimp-image-annotator
gimp-image-annotator or GIÀ, a lightweight GIMP plug-in to alllow for computer vision-assisted image annotation using the powerful GIMP selection toolbox.
Installation
Follow the guide here: https://en.wikibooks.org/wiki/GIMP/Installing_Plugins to find how to install GIMP plug-ins on your system, save the file image-annotator.py
in GIMP's plug-in folder.
In GIMP v2.x, the plug-in system relies on deprecated python2. On Windows, a version of python2 is included in ...
Article abstract
Permeability is an important molecular property in drug discovery, as it co-determines pharmacokinetics whenever a drug crosses the phospholipid bilayer, e.g., into the cell, in the gastrointestinal tract or across the blood-brain barrier. Many methods for the determination of permeability have been developed, including cell line assays, cell-free model systems like PAMPA mimicking, e.g., gastrointestinal epithelia or the skin, as well as the Black lipid membrane (BLM) and ...
M6Allele Pipeline & M6Allele algorithm
Introduction
We have developed an algorithm called M6Allele for identifying allele-specific m6A modifications. To facilitate its usage by researchers, we have also encapsulated our analysis process into a pipeline. You can learn more about the pipeline and the algorithm's usage from the following two modules:
M6Allele Pipeline
PARAMETER INTRODUCTION
-g/--gtf
: ...
EnrichDO
EnrichDO is a double weighted iterative model by integrating the DO graph topology on a global scale. It was based on the latest annotations of the human genome with DO terms, and double weighted the annotated protein-coding genes. On one hand, to reinforce the saliency of direct gene-DO annotations, different initial weights were assigned to directly annotated genes and indirectly annotated genes, respectively. On the other hand, to detect locally most significant node between ...
GALOP - Genome Assembly using Long reads Pipeline
This repository contains an exact copy of the standard Genoscope long reads assembly pipeline.
At the moment, this is not intended for users to download as it uses grid submission commands that will only work at Genoscope. As time goes on, we intend to make this pipeline available to a broader audience. However, genome assembly and polishing commands are accessible in the lib/assembly.py
and lib/polishing.py
files.
galop.py -h
Mandatory
...
cfDNA UniFlow is a unified, standardized, and ready-to-use workflow for processing whole genome sequencing (WGS) cfDNA samples from liquid biopsies. It includes essential steps for pre-processing raw cfDNA samples, quality control and reporting. Additionally, several optional utility functions like GC bias correction and estimation of copy number state are included. Finally, we provide specialized methods for extracting coverage derived signals and visualizations comparing cases and controls. ...
This is an aggregation of the work done in Seq4AMR consisting of the following workflows:
- WF1: AbritAMR / AMRFinderPlus
- WF2: Sciensano (not currently included)
- WF3: SRST2
- WF4: StarAMR
Installation
- You will need to:
- run the [RGI Database ...