Stars
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Perform spa typing on Staphylococcus aureus assemblies or reads.
Toolbox to predict antimicrobial activity of peptides
Microbial-Ecology-Group / Antimicrobial-drug-use-effect-on-microbiome-and-resistome-of-beef-feedlots
This repository contains all of the code required to replicate the analysis in the manuscript "METAGENOMIC INVESTIGATION OF THE EFFECTS OF ANTIMICROBIAL DRUG USE PRACTICES ON THE MICROBIOME AND RES…
AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.
A pipeline for running AMRfinderPlus and collating results into functional classes
Accelerated BLAST compatible local sequence aligner.
Cytoscape: an open source platform for network analysis and visualization
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
The second version of the Kraken taxonomic sequence classification system
Collection of python scripts used in the analysis of long and short read metagenomic data. Includes scripts for taxonomic analysis as well functional annotation of WGS and proteomic data
Workflow for Metagenomics assembly with Long reads And Short reads to recover prokaryotic metagenomics-assembled genomes.
Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
A fast tool for hybrid genome assembly of long and short reads
A hybrid assembly and MAG recovery pipeline (and more!)
Pipeline for hybrid assembly using short and long reads.
Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
A robust, extensible metagenomics pipeline
Infectious Disease Sequencing Platform
A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA