# HG changeset patch # User kkonganti # Date 1657658943 14400 # Node ID 2d0e3b6c693a2bead5425b5648cb85f71dad5135 # Parent aa9d2deb99bd316d60c720b9fb1cb546b2ad665f "planemo upload" diff -r aa9d2deb99bd -r 2d0e3b6c693a cfsan_centriflaken.xml --- a/cfsan_centriflaken.xml Tue Jul 12 16:44:29 2022 -0400 +++ b/cfsan_centriflaken.xml Tue Jul 12 16:49:03 2022 -0400 @@ -116,7 +116,7 @@ Centriflaken suite of automated data analysis pipelines are based on Nextflow DSL2 developed at CFSAN, FDA. These pipelines allow rapid and effective construction of metagenomic assembled genomes (MAGs) to enable bacterial source-tracking. It is based on methods described in our -previous publication (<a href="https://doi.org/10.1371/journal.pone.0245172" target="_blank">Maguire *et al*, 2021</a>). +previous publication (Maguire *et al*, 2021. doi: https://doi.org/10.1371/journal.pone.0245172). ---- @@ -127,7 +127,7 @@ The CPIPES - Centriflaken Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads or long reads, generates MAGs and performs in silico-based analysis (i.e., virulence gene finding). Additionally, AMR gene finding analysis is also included in Centriflaken and performed on MAGs of interest. The final summary plots and tables can be downloaded from the provided MultiQC HTML report generated as part of the pipeline. -The Centriflaken pipeline was validated with data from our previously published method (Maguire *et al*, 2021) and was able to replicate the detection +The Centriflaken pipeline was validated with data from our previously published method (Maguire *et al*, 2021. doi: https://doi.org/10.1371/journal.pone.0245172) and was able to replicate the detection and classification of STECs for each sample. We tested the pipeline with Nanopore data obtained from 21 additional enriched samples from irrigation water and was able to perform the entire precision metagenomics analysis in less than 5 hours for all of them. All the original testing and validation was done on the command line on the CFSAN Raven2 HPC Cluster.