gbouras13

George Bouras's starred repositories

foldcomp

Compressing protein structures effectively with torsion angles

Language:C++GPL-3.0149 5 40

Polypolish

a short-read polishing tool for long-read assemblies

Language:RustGPL-3.0139 11 21

pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Language:CythonGPL-3.0133 7 51

sylph

ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.

Language:RustMIT129 3 14

fitzRoy

A set of functions to easily access AFL data

Language:RNOASSERTION128 18 175

write-the

AI-powered Documentation and Test Generation Tool

Language:PythonMIT91 3 20

AllTheBacteria

Follow up to Grace Blackwell's 661k dataset, for 2023

Language:PythonMIT71 19 24

foldmason

Multiple Protein Structure Alignment at Scale with FoldMason

Language:CGPL-3.059 4 4

zol

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

Language:PythonBSD-3-Clause43 2 5

MicrobeMod

A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing

Language:PythonMIT34 4 22

Bactabolize

Language:PythonGPL-3.03100

Metagenomic-DeepFRI

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

Language:PythonGPL-3.030 5 39

aaanalysis

Python framework for interpretable protein prediction

Language:Jupyter NotebookBSD-3-Clause30 6 5

snk

Snakemake workflow management system and CLI generation tool

Language:PythonMIT29 4 67

pling

Plasmid analysis using rearrangement distances

Language:PythonMIT26 6 35

chainsaw

Language:PythonMIT26 5 16

kmertools

kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML and more

Language:RustGPL-3.025 20

sphae

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

Language:PythonMIT22 5 7

ORForise

Comparison pipeline for Prokaryote Protein Coding Gene Predictors

Language:PythonGPL-3.022 5 11

mini3di

A NumPy port of the foldseek code for encoding protein structures to 3di.

Language:PythonGPL-3.021 2 2

plaque_size_tool

A tool to measure bacteriophages plaque sizes

Language:PythonApache-2.01600

pyrodigal-gv

A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.

Language:PythonGPL-3.013 2 1

tracs

Fast pairwise transmission inference from single genome and/or metagenomic data

Language:Python1300

LDWeaver

Genomewide Epistasis Analysis on Bacteria

Language:RGPL-3.012 2 1

codoff

codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.

Language:PythonBSD-3-Clause9 20

Circular-Contig-Extractor

Language:PythonGPL-3.08 30

unicore

Universal and efficient core gene phylogeny with Foldseek and ProstT5

Language:RustGPL-3.0700

metagenomic_binning_review

Code used to analyse and plot metadata of metagenomic binning tools

Language:Jupyter NotebookMIT5 10

ONT-assembler-benchmark

Language:PythonGPL-3.0500

distribin

Distributed metagenomic binning

Language:PythonMIT1 10