centriflaken is an automated precision metagenomics workflow for assembly and in silico analyses of food-borne pathogens. centriflaken primarily fine-tuned for detecting and classifying Shiga toxin-producing Escherichia coli (STEC), can also be used for performing analyses on other food-borne pathogens such as Salmonella enterica. centriflaken takes as input a UNIX path to FASTQ, generates MAGs, and performs in silico-based analysis for STECs as described in Maguire et al. 2021.
centriflaken works on both Illumina short reads and Oxford Nanopore long reads.
It is written in Nextflow and is part of the modular data analysis pipelines at HFP.
CPIPES:
Manuscript in preparation.
centriflaken: an automated data analysis pipeline for assembly and in silico analyses of food-borne pathogens from metagenomic samples.
Kranti Konganti, Julie Kase, and Narjol Gonzalez-Escalona.
- Incorporation of ANI methods to speed up the analysis methods.
- Incorporation of Oxford Nanopore models for barcode level assembly.
- The main workflow has been used for research purposes only.
- Analysis results should be interpreted with caution.
HFP, FDA assumes no responsibility whatsoever for use by other parties of the Software, its source code, documentation or compiled or uncompiled executables, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic. Further, HFP, FDA makes no representations that the use of the Software will not infringe any patent or proprietary rights of third parties. The use of this code in no way implies endorsement by the HFP, FDA or confers any advantage in regulatory decisions.
