Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison cfsan_bettercallsal.xml @ 16:b90e5a7a3d4f

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"planemo upload"
author kkonganti
date Thu, 07 Sep 2023 15:22:10 -0400
parents 749faef1caa9
children 0e7a0053e4a6
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15:1972677994a6 16:b90e5a7a3d4f
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154 **Testing and Validation** 154 **Testing and Validation**
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156 The CPIPES - bettercallsal Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads list as an input 156 The CPIPES - bettercallsal Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads list as an input
157 and generates a MultiQC report in the final step. The pipeline has been tested on 2x300 bp MiSeq and 2x150 bp NextSeq simulated reads and has been shown to call multiple 157 and generates a MultiQC report in the final step. The pipeline has been tested on 2x300 bp MiSeq and 2x150 bp NextSeq simulated reads and has been shown to call multiple Salmonella serotypes with up to ~95% accuracy. The pipeline has also been tested on metagenomics data sets from Peach and Papaya outbreaks as discussed in our publication (https://www.frontiersin.org/articles/10.3389/fmicb.2023.1200983/full). All the original testing and validation was done on the command line on the CFSAN Raven2 HPC Cluster.
158 Salmonella serotypes with up to ~95% accuracy. The pipeline has also been tested on metagenomics data sets from Peach and Papaya outbreaks as discussed in
159 our preprint (https://www.biorxiv.org/content/10.1101/2023.04.06.535929v1.full). All the original testing and validation was
160 done on the command line on the CFSAN Raven2 HPC Cluster.
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