Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison cfsan_bettercallsal.xml @ 10:1b9de878b04a

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"planemo upload"
author kkonganti
date Thu, 15 Jun 2023 11:16:45 -0400
parents 22165d5e5e0a
children 749faef1caa9
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9:a492d1511fb6 10:1b9de878b04a
146 .. class:: infomark 146 .. class:: infomark
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148 **Testing and Validation** 148 **Testing and Validation**
149 149
150 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 150 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
151 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 shown to call multiple 151 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
152 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 152 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
153 our preprint (https://www.biorxiv.org/content/10.1101/2023.04.06.535929v1.full). All the original testing and validation was 153 our preprint (https://www.biorxiv.org/content/10.1101/2023.04.06.535929v1.full). All the original testing and validation was
154 done on the command line on the CFSAN Raven2 HPC Cluster. 154 done on the command line on the CFSAN Raven2 HPC Cluster.
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