Workflow for Illumina Quality Control and Filtering

Multiple paired datasets will be merged into single paired dataset.

Summary:

• FastQC on raw data files
• fastp for read quality trimming
• BBduk for phiX and (optional) rRNA filtering
• Kraken2 for taxonomic classification of reads (optional)
• BBmap for (contamination) filtering using given references (optional)
• FastQC on filtered (merged) data

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default ...

MoMofy

Module for integrative Mobilome prediction

Bacteria can acquire genetic material through horizontal gene transfer, allowing them to rapidly adapt to changing environmental conditions. These mobile genetic elements can be classified into three main categories: plasmids, phages, and integrons. Autonomous elements are those capable of excising themselves from the chromosome, reintegrating elsewhere, and potentially modifying the host's physiology. Small integrative elements like insertion ...

RASflow: RNA-Seq Analysis Snakemake Workflow

RASflow is a modular, flexible and user-friendly RNA-Seq analysis workflow.

RASflow can be applied to both model and non-model organisms. It supports mapping RNA-Seq raw reads to both genome and transcriptome (can be downloaded from public database or can be homemade by users) and it can do both transcript- and gene-level Differential Expression Analysis (DEA) when transcriptome is used as mapping reference. It requires little programming skill for ...

The containerised pipeline for profiling shotgun metagenomic data is derived from the MGnify pipeline raw-reads analyses, a well-established resource used for analyzing microbiome data. Key components:

• Quality control and decontamination
• rRNA and ncRNA detection using Rfam database
• Taxonomic classification of SSU and LSU regions
• Abundance analysis with mOTUs

Introduction

wombat-p pipelines is a bioinformatics analysis pipeline that bundles different workflow for the analysis of label-free proteomics data with the purpose of comparison and benchmarking. It allows using files from the proteomics metadata standard SDRF.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses ...

SNP-Calling

GATK Variant calling pipeline for genomic data using Nextflow

Quickstart

Install Nextflow using the following command:

curl -s https://get.nextflow.io | bash

Index reference genome:

$ bwa index /path/to/reference/genome.fa

$ samtools faidx /path/to/reference/genome.fa

$ gatk CreateSequenceDictionary -R /path/to/genome.fa -O genome.dict

Launch the pipeline execution with ...

IGVreport-nf

• Description
• Diagram
• User guide
• Workflow summaries
• Metadata
• Component tools
• Required (minimum) inputs/parameters
• Additional notes
• Help/FAQ/Troubleshooting
• Acknowledgements/citations/credits

Description

Quickly generate [IGV .html ...

ROIforMSI

Source codes for manuscript "Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation"

"ExampleWorkflow.ipynb" is a methods document to demonstrate the workflow of our multimodal fusion-based spatial segmentation.

"Utilities.py" contains all the tools to implement our method.

"gui.py" and "registration_gui.py" are files to implement linear and nonlinear registration.

(Licence: GPL-3)

To discover causal mutations of inherited diseases it’s common practice to do a trio analysis. In a trio analysis DNA is sequenced of both the patient and parents. Using this method, it’s possible to identify multiple inheritance patterns. Some examples of these patterns are autosomal recessive, autosomal dominant, and de-novo variants, which are represented in the figure below. To elaborate, the most left tree shows an autosomal dominant inhertitance pattern where the offspring inherits a faulty ...

We present an R script that describes the workflow for analysing honey bee (Apis mellifera) wing shape. It is based on a large dataset of wing images and landmark coordinates available at Zenodo: https://doi.org/10.5281/zenodo.7244070. The dataset can be used as a reference for the identification of unknown samples. As unknown samples, we used data from Nawrocka et al. (2018), available at Zenodo: https://doi.org/10.5281/zenodo.7567336. Among others, the script can be used to identify the geographic ...