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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
author rakesh4osdd
date Wed, 30 Jun 2021 07:13:29 +0000
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1 # clsi_profile
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3 CLSI profile for ASIST using the CLSI standards 2020 by AST profiling for bacteria. It help to generate the input file for ASIST program based on MIC values provided by CLSI based AST profiling.
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5 # ASIST: Antimicrobial Susceptibility standards
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7 In the first column strain names will be mentioned, the second column will be left blank for getting resistance phenotype, starting two rows will comprise antibiotic names (first row) and antibiotic classes (second row). The data for the resistance profile will then start from the C3 column of an excel file which can be converted into a .csv file. Since B3 is left blank, after implementing the algorithm, column B3 will be filled with the resistance phenotype (susceptible, MDR, XDR, PDR).
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9 **Example Input CSV file:**
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11 Strain name,Resistance_phenotype,Antibiotic_A1,Antibiotic_A2,Antibiotic_A_N
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12 Strain_1,Phenotype_1,Resistant,Resistant,Resistant
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13 Strain_2,Phenotype_2,Resistant,Susceptible,Resistant
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15 Link to the code : https://github.com/rakesh4osdd/clsi_profile , https://github.com/rakesh4osdd/asist
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18 # ASIST tool suite
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20 These tools can be install from Galaxy toolshed to a Galaxy installation https://galaxyproject.org/admin/get-galaxy/.