Workflow for long read quality control, contamination filtering, assembly, variant calling and annotation.

• Preprocessing of reference file
• LongReadSum before and after filtering (read quality control)
• Filtlong filter on quality and length
• Flye assembly
• Minimap2 mapping of reads and assembly
• Clair3 variant calling of reads
• Freebayes variant calling of assembly
• Optional Bakta annotation of genomes with no reference
• SnpEff building or downloading of a database
• SnpEff functional ...

Workflow for preprocessing the reference file. Downloads the GenBank file from NCBI if not provided, concatenates plasmid GenBank file(s) with each other and the reference file, extracts GFF3 from the (merged) reference.

This workflow on WorkflowHub: https://workflowhub.eu/workflows/1818

All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/ssb/automated-data-analysis/cwl/-/tree/main/tools Workflows: https://git.wur.nl/ssb/automated-data-analysis/cwl/-/tree/main/workflows ...

Citation

If you use this workflow in your research, please cite it. Use the "Cite this repository" button on the GitHub repository page (generated from CITATION.cff), or cite the archived release on ...

Automated image processing from movies to 2D classification. Includes quality and curator micrgographs protocols as Dose analysis, maxshift, tilt analysis, categorize micrographs, ctf consensus, also include particle curator as Remove duplicates and Deep micrograph cleaner. It also include a support branch to calculate the Box Size and train a model to pick the particles. The list of plugins required are: pwem, xmipp3, motioncorr, miffi, cistem, emfacilities, sphire, gautomatch, relion, repic ...

Introduction

https://github.com/rodtheo/nf-core-assemblyeval

Assemblyeval accepts genome assemblies (FASTA), paired-end Illumina reads, and long reads (ONT or PacBio) via a YAML samplesheet, optionally cleaning them of contamination before evaluation. The pipeline systematically assesses contiguity (QUAST), completeness (COMPLEASM/BUSCO, Merfin), and correctness (ALE, REAPR, CRAQ) — combining read-alignment-based and k-mer-based evidence ...

Bioimaging Data Management Workflow for Plasma Medicine

This repository contains the Jupyter notebook implementation of a bioimaging data management workflow for plasma medicine (see preprint and poster). The workflow is implemented as a structured pipeline integrating open-source tools, including OMERO for image data management, eLabFTW ...

EXCON (v2.3.2)

A Nextflow pipeline for gene family EXpansion and CONtraction analysis across multiple species using CAFE5.

Given a set of genome assemblies and annotations, EXCON builds orthogroups with OrthoFinder, fits and compares multiple CAFE models to identify gene families evolving at significantly different rates, and automatically selects the best-fitting model for downstream analysis. Optionally, GO enrichment analysis can be run on expanded and contracted gene families, and ...

Phorager

Prophage Analysis Pipeline

A comprehensive pipeline for bacterial genome quality control, prophage detection, and prophage characterization

Authors:

• Xena Dyball
• James Docherty
• Alise Ponsero
• Ryan Cook

Citation: [Paper Citation or Preprint Link]

Overview

Phorager provides an integrated workflow for:

• Bacterial genome quality control - CheckM2 assessment, filtering, and dRep dereplication
• Prophage detection - GenoMAD and ...

CLIP-seq Workflow

A Nextflow workflow for end-to-end processing of CLIP-seq data, supporting multiple CLIP protocols.

Overview

Starting from raw FASTQ files (or un-demultiplexed iCLIP data), the workflow processes reads through quality control, adapter trimming, rRNA removal, genome alignment, and UMI deduplication, then runs shoji to extract crosslink sites and produce per-sample and combined count matrices ready for differential binding analysis (see ...

Petrisnake: A secondary analysis pipeline for PETRI-seq data.

This is a Snakemake pipeline for the secondary computational analysis of single cell RNA-seq data from the PETRI-seq protocol (https://www.nature.com/articles/s41564-020-0729-6 and https://www.nature.com/articles/s41586-024-08124-2), this is: From the input FASTQ files, this workflow constructs a gene count table showing the expression of each gene in each cell. Petrisnake is available on WorkflowHub (https://workflowhub.eu/workflows/2081). ...