Please check out this new platform: "Recentrifuge, Robust comparative analysis and contamination removal for metagenomics"

[Rachid]

Dear CLARK users,

Please be aware of this new tool now available (message from the author Jose Manuel Martí):

Recentrifuge (www.recentrifuge.org) is a tool recently published in PLOS Computational Biology (https://doi.org/10.1371/journal.pcbi.1006967) able to analyze results from CLARK using interactive charts with emphasis on the confidence level of the classifications. 

This parallel software implements a robust method for the removal of negative-control and crossover taxa from the rest of the samples, as well as a new comparative analysis engine. Recentrifuge is especially useful in the case of low microbial biomass metagenomic studies or when a more reliable detection of minority organisms is needed, like in clinical, environmental and forensic analysis. Recentrifuge currently supports full-mode output of CLARK, CLARK-l, and CLARK-S. It has a comprehensive user manual that details how to use it for analyzing CLARK's output (https://github.com/khyox/recentrifuge/wiki/Running-recentrifuge-for-CLARK). 

Best,

Rachid