CCDM Bioinformatics

BioDendro

A package to cluster and visualise MS/MS spectral data

predector

Effector prediction pipeline based on protein properties.

catastrophy

CATAStrophy predicts filamentous plant pathogen lifestyle characteristics based on their CAZyme composition.

barley-pow-rnaseq

Barley Baudin and Palace NIL RNAseq analysis during powdery mildew infection

catastrophy-pipeline

Easily run the CATAStrophy classifier on many genomes.

LR-toolkit

🌱 Toolkit for long reads RNAseq data analysis

slurm_scripts

SLURM script collection

20200306-pnodorum_pangenome_pseudocode

Code accompanying an upcoming manuscript on a P. nodorum pangenome.

ccdmb.github.io

Front page for the CCDM bioinformatics group.

nanopore_assembly

panann

Pipelines for gene and TE annotation of pangenomes.

PathoPore

PathoPore - Longer Sequences and NextFlow Faster Analysis

qcflow

Perform basic QC on illumina data

qcflow-rnaseq

:white_check_mark: :rotating_light: QC and alignement pipeline for RNA-seq reads

R_Script_templates

Example templates for bioinformatics analyses

snptree

A nextflow pipeline to run phylogenetic analyses using SNPs

wheat-agr-tanspot

RNA-seq analysis of wheat AGR during tan spot infection

barley-DH-pow-rnaseq

RNA-seq analysis of barley double haploid (DH) lines from Baudin / Eth069 cross during powdery mildew disease

mitoflow

A small pipeline for assembling mitochondrial genomes and filtering reads prior to assembly.

mumflow

A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.

pante

A pipeline for predicting and masking transposable elements in multiple genomes.

pclust

A nextflow pipeline to cluster sets of proteins.

postasm

QC and tidying on assembled genomes.

predector-data

Datasets used for developing the predector pipeline

predector-utils

Utilities for running the predector pipeline.

PTR-60

PTR gene analysis for race 2 and 4 isolates PacBio sequenced