Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.

This is a deep learning method for identification of viral contigs with short length from metagenomic data.

De novo assembler for single molecule sequencing reads using repeat graphs

A preprocessing pipeline for ONT data

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Official repository for the QIIME 2 framework.

StaG Metagenomic Workflow Collaboration

Interactively explore metagenomes and more from a web browser.

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

💾 📃 "Reads to report" for public health and clinical microbiology

🌈 Interactive analysis of metagenomics data