Kraken2 - Johns Hopkins University
Sep 29, 2022 · As of September 2020, we have created a Amazon Web Services site to host many of the most widely-used Kraken2 indices, available at https://github.com/BenLangmead/aws-indexes. Publications The Kraken 2 paper has been published in Genome Biology as of November 28th, 2019: Improved metagenomic analysis …
Kraken 2 Databases - Johns Hopkins University
Maxikraken2 and Kraken2-microbial databases. These databases are maintained by LomanLab. More information at the link provided.
Kraken2 Protocol - Johns Hopkins University
This page describes the Kraken2 protocol detailed in the Nature Protocols paper titled Metagenome analysis using the Kraken software suite. Published on September 28, 2022, the protocol explains how Kraken 2, Bracken, KrakenUniq, and KrakenTools are used for both microbiome analysis and pathogen detection.
Kraken2 - Johns Hopkins University
Maxikraken2 and Kraken2-microbial databases. These databases are maintained by LomanLab. More information at the link provided.
Kraken2 - Johns Hopkins University
CCB » Software » Kraken2 Home; Manual; Downloads; Kraken 2 taxonomic sequence classification system As of 06/05/2020, the manual is located in the Kraken 2 Github Wiki. The Center for Computational Biology at Johns Hopkins University. CCB Software;
About Kraken - Johns Hopkins University
Sep 29, 2022 · About Kraken. Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but …
How to Choose Your Metagenomics Classification Tool
Sep 29, 2022 · He incorporated the KrakenUniq kmer-counting features in Kraken2. He also led the effort for the Kraken Nature Protocols Paper. ( Steinegger Lab webpage ) Ben Langmead (BL) is an Associate Professor at Johns Hopkins University in the Department of Computer Science.
Kraken Manual - Johns Hopkins University
Introduction. Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers.This database contains a mapping of every k-mer in Kraken's genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer.
KrakenTools - Johns Hopkins University
Dec 10, 2020 · KrakenTools is a suite of individual scripts designed for use with Kraken, KrakenUniq, Kraken2, and Bracken. These scripts provide users of the above classification/abundance estimation tools additional support primarily for downstream analysis of Kraken/Bracken results.
Bracken - Johns Hopkins University
Aug 7, 2019 · As part of the Kraken2 and MiniKraken2 release, we are also releasing pre-built Bracken files that are compatible with MiniKraken2. See Downloads for download links and details. 09/10/2018 - v2.0.0 release