This workflow was developed for the 2024 Bioinformatics Bootcamp at The Open University. It imports datasets from the EBI SCXA, reformats then, and analyses them similar to the Filter, plot and explore Galaxy tutorial.

PVGA is a powerful virus-focused assembler that does both assembly and polishing. For virus genomes, small changes will lead to significant differences in terms of viral function and pathogenicity. Thus, for virus-focused assemblers, high-accuracy results are crucial. Our approach heavily depends on the input reads as evidence to produce the reported genome. It first adopts a reference genome to start with. We then align all the reads against the reference genome to get an alignment graph. After ...

Current version of this workflow: https://workflowhub.eu/workflows/1109. Please use only with the new version. KNIME workflow to gather ChEMBL permeability data is availbale: https://workflowhub.eu/workflows/1169.

gSpreadComp: Streamlining Microbial Community Analysis for Resistance, Virulence, and Plasmid-Mediated Spread

Overview

gSpreadComp is a UNIX-based, modular bioinformatics toolkit designed to streamline comparative genomics for analyzing microbial communities. It integrates genome annotation, gene spread calculation, plasmid-mediated horizontal gene transfer (HGT) detection and resistance-virulence ranking within the analysed microbial community to help researchers identify potential ...

Code for the high risk autism phenotype paper

Much of the code in this repo originated from ASD High Risk Endophenotype Code Supplement and was written by Sebastian Urchs and Hien Nguyen.

Data availability

All data to reproduce the analysis can be downloaded from ...

AnnoAudit - Annotation Auditor

AnnoAudit is a robust Nextflow pipeline designed to evaluate the quality of genomic annotations through a multifaceted approach.

Overview of the workflow

The workflow assess the annotation quality based on different criteria:

• Protein evidence support
• RNASeq evidence support
• Statistics of the predictions (i.e., gene length, exon number, etc.)
• Ortholog analysis (BUSCO, OMArk)

Input data

• Reference genome genome.[.fna, .fa, .fasta]
• Annotation ...

Prostate cancer classification workflow

This workflow segments tissue regions and classifies prostate cancer on H&E whole slide images, using AI. It consists of three steps:

1. low-resolution tissue segmentation to select areas for further processing;

2. high-resolution tissue segmentation to refine borders - it uses step 1 as input;

3. high-resolution normal/cancer classification - it uses step 1 as input.

Tissue segmentation workflow

This workflow performs tissue segmentation on H&E whole slide images using AI.

PISAD - Phsaed Intraspecies Sample Anomalies Detection tool

Summary

We developed PISAD, a tool designed to detect anomalies in cohort samples without requiring reference information. It is primarily divided into two stages. Stage 1: We select low-error data from the cohort and conduct reference-free SNP calling to construct a variant sketch. Stage 2: By comparing the k-mer counts of other cohort data to the variant sketch, we infer the relationships between the sample and other samples to ...