George Bouras

pharokka. Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.

phold. Phage Annotation using Protein Structures

hybracter. Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

dnaapler. Reorients assembled microbial sequences

plassembler. Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates

baktfold. Rapid & standardized genome annotation using protein structural information

pypolca. Standalone Python re-implementation of the POLCA polisher from MaSuRCA

coatofarms. ONT Long-read 16S Snakemake pipeline using Emu

colabfoldv. Augmented Local MSA Generation for Phage and Viral Proteins using the ColabFold Framework

Useful_Scripts. Collection of Useful Scripts

megapharokka. A fork of Pharokka to handle enVhogs

taxanalyser. Snakemake and Snaketool pipeline to taxonomically profile ONT long read metagenomics data

CRS_Saureus_Evolutionary_Landscape. Repository to Hold Code base for 'The Intra-Host Evolutionary Landscape And Pathoadaptation Of Persistent Staphylococcus aureus In Chronic Rhinosinusitis' Paper

Nanopore_Bacterial_Assembly_Pipeline. Pipeline to assemble many bacterial assemblies from Nanopore data

distill_prostt5. Distillation Commands for ProstT5

ABACBS2024-GPU-workshop-demo-plm-training-slurm-setonix. ABACBS 2024 GPU Workshop Demonstration PyTorch + Slurm scripts to Post-Train ESM-2

16S_Emu_Pipeline. Python

WGS_TCGA_Kraken_Pipeline. Pipeline to Extract Contaminant Reads from TCGA WGS Datasets

phold-lib. Shared pLM inference library for phold and baktfold

NanoReceptor. Program to infer IG and TRA quantities from Long Read RNA-Seq Data

Nanopore_RNA_Seq_cdna_Pipeline. Python

phold-plot-wasm-app. HTML

alphafold3. AlphaFold 3 inference pipeline.