FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

A pipeline to investigate horizontal gene transfer from NGS data

A simple nextflow pipeline for running kraken2 and bracken in a docker container

Calculate confidence scores from Kraken2 output

A post-processing tool to reclassify Kraken 2 output based on the confidence score and/or minimum minimizer hit groups.

A Shiny app for taxonomic abundance visualization

A bare-bones, ridiculously simple metagenomics pipeline for viruses using Kraken 2 written in Nextflow.

Creates a simple OTU table from Kraken2 report.

Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species

a simple python script for "grafting" on novel sequences to a custom Kraken2 database

This script filters low abundant reads from Bracken outputs for downstream analyses

An awesome BCL demultiplexing and FastQ quality-control pipeline

#Scripts to create Kraken2 database of PAFTOL V2.0 Angio353 genes. An excellent database for taxonomic identification of plants. #https://treeoflife.kew.org/ #https://github.com/DerrickWood/kraken2/wiki #Prior to using this script, download and install kraken2 and make sure it is working and in your PATH. #Make sure the location of the python sc…

An intuitive tutorial on Kraken2 metagenomic analysis

A Docker image for the conifer utility.

Kraken2.0.7-beta edited

A LatchBio workflow for running Kraken2