gbouras13

coatofarms

ONT Long-read 16S Snakemake pipeline using Emu

dnaapler

Reorients assembled microbial sequences

hybracter

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

megapharokka

A fork of Pharokka to handle enVhogs

Nanopore_Bacterial_Assembly_Pipeline

Pipeline to assemble many bacterial assemblies from Nanopore data

pharokka

fast phage annotation program

phold

Phage Annotation using Protein Structures

plassembler

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

pypolca

Standalone Python re-implementation of the POLCA polisher from MaSuRCA

Useful_Scripts

Collection of Useful Scripts

gbouras13/pharokka

fast phage annotation program

gbouras13/dnaapler

Reorients assembled microbial sequences

gbouras13/hybracter

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

gbouras13/phold

Phage Annotation using Protein Structures

gbouras13/plassembler

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

gbouras13/pypolca

Standalone Python re-implementation of the POLCA polisher from MaSuRCA

gbouras13/coatofarms

ONT Long-read 16S Snakemake pipeline using Emu

gbouras13/Useful_Scripts

Collection of Useful Scripts

gbouras13/megapharokka

A fork of Pharokka to handle enVhogs

gbouras13/Nanopore_Bacterial_Assembly_Pipeline

Pipeline to assemble many bacterial assemblies from Nanopore data

gbouras13/taxanalyser

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

gbouras13/16S_Emu_Pipeline

gbouras13/WGS_TCGA_Kraken_Pipeline

Pipeline to Extract Contaminant Reads from TCGA WGS Datasets

gbouras13/NanoReceptor

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

gbouras13/hybracter_benchmarking

Benchmarking Pipeline for Hybracter

gbouras13/single_marker_gene_microbiome_analysis

Repository to hold analysis for single marker genes in HNSC Microbiome

gbouras13/Acanthophis

A comprehensive, opinionated plant variant calling pipeline in Snakemake

gbouras13/alphafold3-pytorch

Implementation of Alphafold 3 in Pytorch

gbouras13/bioconda-recipes

Conda recipes for the bioconda channel.

gbouras13/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

gbouras13/depth_vs_polishing_analysis

Repository to hold code and data for the How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies manuscript

gbouras13/giantpandrna

ONT Long-read cDNA quanitification pipeline using Bambu

gbouras13/hafeZ

A tool for identifying active prophage elements through read mapping

gbouras13/Koverage

Quickly get coverage statistics given reads and an assembly

gbouras13/Phynteny

Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny

gbouras13/plassembler_simulation_benchmarking

Benchmarking and Simulation Scripts for Plassembler

gbouras13/ProstT5

Bilingual Language Model for Protein Sequence and Structure

gbouras13/rasusa

Randomly subsample sequencing reads or alignments

gbouras13/S_Aureus_Analysis_Pipeline

Analysis of S Aureus WGS Isolates

gbouras13/sphae

Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!