Introduction

CBRA (CIBERER Bioinformatics for Rare diseases Analysis) is a workflow optimized for the analysis of rare diseases, designed to detect SNVs, INDELs, CNVs and SVs in targeted sequencing data (CES/WES) as well as whole genome sequencing (WGS).

This pipeline is developed using Nextflow, a workflow management system that enables an easy execution across various computing environments. It uses Docker or Singularity containers, simplifying setup and ensuring reproducibility of results. ...

Honey bees (Apis mellifera) are essential pollinators supporting agricultural production and wild plant diversity. In evolutionary lineage M, some populations are threatened by genetic erosion caused by the widespread introduction of commercially bred queens. To assess this risk, wing images from existing and new datasets were used to assign them to four evolutionary lineages (A, C, M, and O). The new dataset consisted of 29,043 wing images representing 1,342 colony samples from ten countries. ...

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 ...

Data from different sources

Workflow for quality assessment and taxonomic classification of amplicon long read sequences. In addition files are exported to their respective subfolders for easier data management in a later stage.

Inputs are expected to be basecalled fastq files

Steps:

• NanoPlot read quality control, before and after filtering
• fastplong read quality and length filtering
• Emu abundance; species-level taxonomic abundance for full-length 16S read

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 ...