A bioinformatics software focused on quality control based on species criteria

A bioinformatics software focused on quality control based on species criteria

The AMRgen package provides tools for interpreting antimicrobial resistance (AMR) genes, integrating genomic data with phenotypic antimicrobial susceptibility testing (AST) data, and calculating ge…

Cutadapt removes adapter sequences from sequencing reads

Python library for time series forecasting using scikit-learn compatible models, statistical methods, and foundation models

The AMRnet dashboard aims to make high-quality, robust and reliable genome-derived AMR surveillance data accessible to a wide audience

Quick and easy outbreak reconstruction pipeline

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

PyAMPA: The new version of the AMPA software

Rapid comparison and dereplication of genomes

interactive & hardware agnostic SDK for lab automation

Small utility script to submit genomes to PHASTER for phage detection

Identify phage regions in bacterial genomes for masking purposes

Python Imaging Library (fork)

Code for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

MLstatkit is a comprehensive Python library designed to seamlessly integrate established statistical methods into machine learning projects.

ARG normalization by mapping to the ARO ontology.

This tool predicts plasmid sequences from genomic and metagenomic assemblies using machine learning.

This repo collects the list of learning online resources related to microbiome computational science and tools.

This repo collects the list of podcasts related to microbiome science: science, microbiology and bioinformatics.

Tools for fast and flexible genome assembly scaffolding and improvement

Feature Extraction Package for Biological Sequences

Wally: Visualization of aligned sequencing reads and contigs

BioAutoML: Automated Feature Engineering and Metalearning

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Pilon is an automated genome assembly improvement and variant detection tool

Frequently used commands in bioinformatics